2EB0 | pdb_00002eb0

Crystal structure of Methanococcus jannaschii putative family II inorganic pyrophosphatase

• PDB DOI: https://doi.org/10.2210/pdb2EB0/pdb

• Classification: HYDROLASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-05 Released: 2007-08-07 
• Deposition Author(s): Shimada, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Methanococcus jannaschii inorganic pyrophosphatase

Shimada, A., Kuramitsu, S., Yokoyama, S.

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.

Macromolecule Content 

• Total Structure Weight: 68.53 kDa 
• Atom Count: 5,204 
• Modeled Residue Count: 611 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Manganese-dependent inorganic pyrophosphatase	A, B	307	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ0608 EC: 3.6.1.1
UniProt
Find proteins for Q58025 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58025  Go to UniProtKB:  Q58025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth B], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.843	α = 90
b = 146.761	β = 90
c = 54.286	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Shimada, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description