3UP8 | pdb_00003up8

Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B

• PDB DOI: https://doi.org/10.2210/pdb3UP8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-17 Released: 2011-12-14 
• Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 67.15 kDa 
• Atom Count: 4,521 
• Modeled Residue Count: 562 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 2,5-diketo-D-gluconic acid reductase B	A, B	298	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: dkgB, R00966, SMc00101 EC: 1.1.1.274
UniProt
Find proteins for Q92RC6 (Rhizobium meliloti (strain 1021)) Explore Q92RC6  Go to UniProtKB:  Q92RC6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.96 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.283	α = 90
b = 88.768	β = 90
c = 123.638	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary