1J3P | pdb_00001j3p

Crystal structure of Thermococcus litoralis phosphoglucose isomerase

• PDB DOI: https://doi.org/10.2210/pdb1J3P/pdb

• Classification: ISOMERASE
• Organism(s): Thermococcus litoralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-02-11 Released: 2004-02-24 
• Deposition Author(s): Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.271 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of a novel cupin-type phosphoglucose isomerase

Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

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: 43.56 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 370 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucose Isomerase	A, B	190	Thermococcus litoralis	Mutation(s): 0  EC: 5.3.1.9
UniProt
Find proteins for P84140 (Thermococcus litoralis) Explore P84140  Go to UniProtKB:  P84140

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.271 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.76	α = 90
b = 82.17	β = 90
c = 125.11	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

Revision History  

• Version 1.0: 2004-02-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations