4KWA

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline

PDB DOI: https://doi.org/10.2210/pdb4KWA/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Saccharomonospora viridis DSM 43017
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-23 Released: 2013-06-12
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259
R-Value Work: 0.199
R-Value Observed: 0.202

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 46.22 kDa
Atom Count: 3,411
Modelled Residue Count: 385
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	195	Saccharomonospora viridis DSM 43017	Mutation(s): 0 Gene Names: Svir_16270
UniProt
Find proteins for C7MT25 (Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / CCUG 5913 / NBRC 12207 / NCIMB 9602 / P101)) Explore C7MT25 Go to UniProtKB: C7MT25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7MT25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHT Query on CHT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	CHOLINE ION C₅ H₁₄ N O OEYIOHPDSNJKLS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.901	α = 90
b = 77.355	β = 90
c = 109.83	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection

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Help and Resources

4KWA

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with choline

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)