4QMB | pdb_00004qmb

The structure of inorganic pyrophosphatase from Schistosoma japonicum

PDB DOI: https://doi.org/10.2210/pdb4QMB/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.263 (Depositor), 0.270 (DCC)
R-Value Work:
0.202 (Depositor), 0.220 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The structure and function of inorganic pyrophosphatase from Schistosoma japonicum

Wu, Q.F.

To be published.

Macromolecule Content

Total Structure Weight: 65.43 kDa
Atom Count: 4,618
Modeled Residue Count: 567
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5DE13
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.263 (Depositor), 0.270 (DCC)
R-Value Work: 0.202 (Depositor), 0.220 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.75	α = 90
b = 75.75	β = 90
c = 122.962	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

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Entry History

Deposition Data

Released Date: 2015-07-15

Deposition Author(s):

Revision History (Full details and data files)

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, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.