3R6S | pdb_00003r6s

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.288 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP

Jungwirth, B., Pojer, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcription regulator	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	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
HEZ	H [auth A], L [auth D], O [auth F]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.288 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.206 (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

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Jungwirth, B., Pojer, F.

Revision History  

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