6C45 | pdb_00006c45

Crystal structure of human inorganic pyrophosphatase in the P212121 space group

PDB DOI: https://doi.org/10.2210/pdb6C45/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-11 Released: 2019-01-16
Deposition Author(s): Niu, H., Zhu, J., Huang, X., Du, Z.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6C45

This is version 1.4 of the entry. See complete history.

Literature

Expression, purification and crystallization of the human protein PPA1

Niu, H., Zhu, J., Huang, X., Du, Z.

To be published.

Macromolecule Content

Total Structure Weight: 130.82 kDa
Atom Count: 9,557
Modeled Residue Count: 1,135
Deposited Residue Count: 1,156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D	289	Homo sapiens	Mutation(s): 0 Gene Names: PPA1, IOPPP, PP EC: 3.6.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15181 (Homo sapiens) Explore Q15181 Go to UniProtKB: Q15181
PHAROS: Q15181 GTEx: ENSG00000180817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15181
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.25	α = 90
b = 136.94	β = 90
c = 216.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM116062-01

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-03-13
Changes: Data collection, Database references
Version 1.4: 2025-11-12
Changes: Data collection, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.