5DAN | pdb_00005dan

Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+

• PDB DOI: https://doi.org/10.2210/pdb5DAN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-20 Released: 2016-09-21 
• Deposition Author(s): Xu, X.
• Funding Organization(s): National Natural Science Foundation of China, Zhejiang Provincial Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+

Xu, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.15 kDa 
• Atom Count: 2,437 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diketo-D-gluconic acid reductase	A	274	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1743, Tmari_1751 EC: 1.1.1
UniProt
Find proteins for Q9X265 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X265  Go to UniProtKB:  Q9X265

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.821	α = 90
b = 84.821	β = 90
c = 93.727	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Xu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570738
National Natural Science Foundation of China	China	31400630
Zhejiang Provincial Natural Science Foundation of China	China	LY14C050002

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description