3DFU | pdb_00003dfu

CRYSTAL STRUCTURE OF A PUTATIVE ROSSMANN-LIKE DEHYDROGENASE (CGL2689) FROM CORYNEBACTERIUM GLUTAMICUM AT 2.07 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3DFU/pdb

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


• Deposited: 2008-06-12 Released: 2008-07-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.223 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of Protein of Unknown Function from the 6-Phosphogluconate Dehydrogenase-Like Family (NP_601885.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.07 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content 

• Total Structure Weight: 51.65 kDa 
• Atom Count: 3,769 
• Modeled Residue Count: 456 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized Protein from 6-Phosphogluconate Dehydrogenase-Like Family	A, B	232	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: NP_601885.1, Cgl2689, cg2976
UniProt
Find proteins for Q8NM90 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NM90  Go to UniProtKB:  Q8NM90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.223 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DFU

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.79	α = 90
b = 47.07	β = 90
c = 63.24	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

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary