6DWE

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and BRD0059-bound form

PDB DOI: https://doi.org/10.2210/pdb6DWE/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-26 Released: 2018-07-11
Deposition Author(s): Chang, C., Michalska, K., Maltseva, N.I., Jedrzejczak, R., McCarren, P., Nag, P.P., Joachimiak, A., Satchell, K., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.202
R-Value Work: 0.155
R-Value Observed: 0.156

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of tryptophan synthase from M. tuberculosis - closed form with BRD6309 bound

Chang, C., Michalska, K., Maltseva, N.I., Jedrzejczak, R., McCarren, P., Nag, P.P., Joachimiak, A., Satchell, K.

To be published.

Macromolecule Content

Total Structure Weight: 293.91 kDa
Atom Count: 20,363
Modelled Residue Count: 2,597
Deposited Residue Count: 2,744
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A, C [auth G], E, G [auth C]	276	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpA, Rv1613, MTCY01B2.05 EC: 4.2.1.20
UniProt
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFY1 Go to UniProtKB: P9WFY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFY1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B, D [auth H], F, H [auth D]	410	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpB, Rv1612, MTCY01B2.04 EC: 4.2.1.20
UniProt
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX9 Go to UniProtKB: P9WFX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P1T Query on P1T Download Ideal Coordinates CCD File SDF format, chain FB [auth D] SDF format, chain OA [auth F] SDF format, chain CA [auth H] SDF format, chain L [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain OA [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain L [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain OA [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain L [auth B]	CA [auth H], FB [auth D], L [auth B], OA [auth F]	2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID C₁₁ H₁₅ N₂ O₇ P BXUDKFHCAMQSRX-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain FB [auth D] Focus chain L [auth B] Focus chain OA [auth F] Interactions & Density Focus chain CA [auth H] Focus chain FB [auth D] Focus chain L [auth B] Focus chain OA [auth F]
HDJ Query on HDJ Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain JA [auth H] SDF format, chain PB [auth D] SDF format, chain V [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain PB [auth D] MOL2 format, chain V [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain PB [auth D] mmCIF format, chain V [auth B]	AB [auth F], JA [auth H], PB [auth D], V [auth B]	(2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile C₁₈ H₁₅ F₃ N₂ OZFKPHFHTNQIQS-XYJFISCASA-N		Interactions Focus chain AB [auth F] Focus chain JA [auth H] Focus chain PB [auth D] Focus chain V [auth B] Interactions & Density Focus chain AB [auth F] Focus chain JA [auth H] Focus chain PB [auth D] Focus chain V [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain QB [auth D] MOL2 format, chain QB [auth D] mmCIF format, chain QB [auth D]	QB [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain QB [auth D] Interactions & Density Focus chain QB [auth D]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain HB [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain DA [auth H] SDF format, chain GB [auth D] SDF format, chain M [auth B] SDF format, chain PA [auth F] MOL2 format, chain HB [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain DA [auth H] MOL2 format, chain GB [auth D] MOL2 format, chain M [auth B] MOL2 format, chain PA [auth F] mmCIF format, chain HB [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain DA [auth H] mmCIF format, chain GB [auth D] mmCIF format, chain M [auth B] mmCIF format, chain PA [auth F]	DA [auth H] GB [auth D] HB [auth D] M [auth B] N [auth B] DA [auth H], GB [auth D], HB [auth D], M [auth B], N [auth B], O [auth B], PA [auth F], QA [auth F], RA [auth F]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Interactions & Density Focus chain DA [auth H] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain MA [auth H] MOL2 format, chain CB [auth F] MOL2 format, chain MA [auth H] mmCIF format, chain CB [auth F] mmCIF format, chain MA [auth H]	CB [auth F], MA [auth H]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain MA [auth H] Interactions & Density Focus chain CB [auth F] Focus chain MA [auth H]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain NA [auth E] SDF format, chain DB [auth C] SDF format, chain I [auth A] SDF format, chain X [auth G] MOL2 format, chain NA [auth E] MOL2 format, chain DB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain X [auth G] mmCIF format, chain NA [auth E] mmCIF format, chain DB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain X [auth G]	DB [auth C], I [auth A], NA [auth E], X [auth G]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain DB [auth C] Focus chain I [auth A] Focus chain NA [auth E] Focus chain X [auth G] Interactions & Density Focus chain DB [auth C] Focus chain I [auth A] Focus chain NA [auth E] Focus chain X [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BB [auth F] MOL2 format, chain BB [auth F] mmCIF format, chain BB [auth F]	BB [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Interactions & Density Focus chain BB [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain W [auth B] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain W [auth B] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain W [auth B]	KA [auth H], LA [auth H], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KA [auth H] Focus chain LA [auth H] Focus chain W [auth B] Interactions & Density Focus chain KA [auth H] Focus chain LA [auth H] Focus chain W [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EB [auth C] SDF format, chain GA [auth H] SDF format, chain KB [auth D] SDF format, chain OB [auth D] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain YA [auth F] SDF format, chain AA [auth G] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain NB [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth G] SDF format, chain ZA [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EB [auth C] MOL2 format, chain GA [auth H] MOL2 format, chain KB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain ZA [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EB [auth C] mmCIF format, chain GA [auth H] mmCIF format, chain KB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain ZA [auth F]	AA [auth G] BA [auth G] EA [auth H] EB [auth C] FA [auth H] AA [auth G], BA [auth G], EA [auth H], EB [auth C], FA [auth H], GA [auth H], HA [auth H], IA [auth H], IB [auth D], J [auth A], JB [auth D], K [auth A], KB [auth D], LB [auth D], MB [auth D], NB [auth D], OB [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], VA [auth F], WA [auth F], XA [auth F], Y [auth G], YA [auth F], Z [auth G], ZA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain EA [auth H] Focus chain EB [auth C] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth G] Focus chain YA [auth F] Focus chain Z [auth G] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain EA [auth H] Focus chain EB [auth C] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth G] Focus chain YA [auth F] Focus chain Z [auth G] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.202
R-Value Work: 0.155
R-Value Observed: 0.156
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.093	α = 90
b = 159.396	β = 90
c = 165.226	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 1.1: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary