2ZKT | pdb_00002zkt

Structure of PH0037 protein from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2ZKT/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-29 Released: 2009-04-21 
• Deposition Author(s): Lokanath, N.K., Pampa, K.J., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.286 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Literature

Structure of PH0037 protein from Pyrococcus horikoshii

Lokanath, N.K., Pampa, K.J., Kunishima, N.

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.32 kDa 
• Atom Count: 5,720 
• Modeled Residue Count: 711 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-independent phosphoglycerate mutase	A, B	412	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: apgM EC: 5.4.2.1 (PDB Primary Data), 5.4.2.12 (UniProt)
UniProt
Find proteins for O57742 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57742  Go to UniProtKB:  O57742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.286 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.9	α = 90
b = 155.9	β = 90
c = 230.857	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Lokanath, N.K., Pampa, K.J., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations