1VP5

Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VP5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-13 Released: 2004-10-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.99 kDa 
• Atom Count: 4,929 
• Modelled Residue Count: 567 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diketo-D-gluconic acid reductase	A, B	298	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1009 EC: 1.1.1.274
UniProt
Find proteins for Q9X0A2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0A2  Go to UniProtKB:  Q9X0A2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VP5

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.314	α = 90
b = 94.314	β = 90
c = 146.855	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-05-22
  Changes: Data collection, Refinement description