2P5U | pdb_00002p5u

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb2P5U/pdb

• Classification: ISOMERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-16 Released: 2007-04-17 
• Deposition Author(s): Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Dillard, B., Chrzas, J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.261 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.226 (DCC) 

Literature

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Dillard, B., Chrzas, J., Rose, J.P., Wang, B.-C.

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)

Macromolecule Content 

• Total Structure Weight: 137.92 kDa 
• Atom Count: 10,139 
• Modeled Residue Count: 1,244 
• Deposited Residue Count: 1,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A, B, C, D	311	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0591 EC: 5.1.3.2
UniProt
Find proteins for Q5SKQ2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKQ2  Go to UniProtKB:  Q5SKQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.261 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.226 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.922	α = 90
b = 250.922	β = 90
c = 121.036	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SGXPRO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Dillard, B., Chrzas, J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations