6C45

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Expression, purification and crystallization of the human protein PPA1

Niu, H., Zhu, J., Huang, X., Du, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Niu, H., Zhu, J., Huang, X., Du, Z.

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

Revision History  

• 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