4LUG | pdb_00004lug

Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb4LUG/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-25 Released: 2014-07-30
Deposition Author(s): Grzechowiak, M., Ruszkowski, M., Sikorski, M., Jaskolski, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.200 (Depositor), 0.205 (DCC)
R-Value Work:
0.155 (Depositor), 0.166 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4LUG

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Inorganic pyrophosphatase PPA1 from Arabidopsis thaliana

Grzechowiak, M., Ruszkowski, M., Sikorski, M., Jaskolski, M.

To be published.

Macromolecule Content

Total Structure Weight: 41.63 kDa
Atom Count: 3,015
Modeled Residue Count: 351
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B	180	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PPa1 EC: 3.6.1.1
UniProt
Find proteins for Q93V56 (Arabidopsis thaliana) Explore Q93V56 Go to UniProtKB: Q93V56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93V56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.200 (Depositor), 0.205 (DCC)
R-Value Work: 0.155 (Depositor), 0.166 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.02	α = 90
b = 82.02	β = 90
c = 175.08	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-30

Deposition Author(s):

Grzechowiak, M.

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.