3R6S

Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP

PDB DOI: https://doi.org/10.2210/pdb3R6S/pdb

Classification: TRANSCRIPTION
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-22 Released: 2012-03-28
Deposition Author(s): Jungwirth, B., Pojer, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.288 (Depositor), 0.280 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP

Jungwirth, B., Pojer, F.

To be published.

Macromolecule Content

Total Structure Weight: 165.48 kDa
Atom Count: 10,745
Modelled Residue Count: 1,345
Deposited Residue Count: 1,482
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcription regulator	A, B, C, D, E A, B, C, D, E, F	247	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: cg0350, cg0350 (glxR), Cgl0291
UniProt
Find proteins for Q79VI7 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q79VI7 Go to UniProtKB: Q79VI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q79VI7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMP Query on CMP 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 K [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	G [auth A] I [auth B] J [auth C] K [auth D] M [auth E] G [auth A], I [auth B], J [auth C], K [auth D], M [auth E], N [auth F]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C₁₀ H₁₂ N₅ O₆ P IVOMOUWHDPKRLL-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth D] SDF format, chain O [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth D] MOL2 format, chain O [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth D] mmCIF format, chain O [auth F]	H [auth A], L [auth D], O [auth F]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth D] Focus chain O [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth D] Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.288 (Depositor), 0.280 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.248	α = 90
b = 111.248	β = 90
c = 186.951	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Jungwirth, B.

Pojer, F.

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description