4QLZ | pdb_00004qlz

The structure of inorganic pyrophosphatase from Schistosoma japonicum

• PDB DOI: https://doi.org/10.2210/pdb4QLZ/pdb

• Classification: HYDROLASE, METAL BINDING PROTEIN
• Organism(s): Schistosoma japonicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-06-13 Released: 2015-07-15 
• Deposition Author(s): Wu, Q.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.270 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Study on the structure and function of inorganic pyrophosphatase from Schistosoma japonicum

Wu, Q.F.

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: 66.09 kDa 
• Atom Count: 4,628 
• Modeled Residue Count: 567 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SJCHGC07024 protein	A, B	287	Schistosoma japonicum	Mutation(s): 1  EC: 3.6.1.1
UniProt
Find proteins for Q5DE13 (Schistosoma japonicum) Explore Q5DE13  Go to UniProtKB:  Q5DE13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.270 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.08	α = 90
b = 76.08	β = 90
c = 123.41	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Wu, Q.F.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Experimental preparation
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description