3MBH | pdb_00003mbh

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

PDB DOI: https://doi.org/10.2210/pdb3MBH/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-25 Released: 2010-06-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.206 (Depositor), 0.220 (DCC)
R-Value Work:
0.167 (Depositor), 0.180 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 201.74 kDa
Atom Count: 15,283
Modelled Residue Count: 1,732
Deposited Residue Count: 1,746
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphomethylpyrimidine kinase	A, B, C, D, E A, B, C, D, E, F	291	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_4458 EC: 2.7.1.35
UniProt
Find proteins for Q89ZB9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZB9 Go to UniProtKB: Q89ZB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89ZB9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PXL Query on PXL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain O [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain O [auth F]	G [auth A] I [auth B] J [auth C] L [auth D] M [auth E] G [auth A], I [auth B], J [auth C], L [auth D], M [auth E], O [auth F]	3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE C₈ H₉ N O₃ RADKZDMFGJYCBB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain N [auth E] SDF format, chain P [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F]	H [auth A], K [auth C], N [auth E], P [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206 (Depositor), 0.220 (DCC)
R-Value Work: 0.167 (Depositor), 0.180 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33MBH

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.723	α = 90
b = 138.368	β = 90
c = 143.539	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Refinement description, Structure summary

Prepare Data

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Deposit Data

Help and Resources

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Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3MBH | pdb_00003mbh