1HUJ

REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT

PDB DOI: https://doi.org/10.2210/pdb1HUJ/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1997-12-26 Released: 1998-04-08
Deposition Author(s): Swaminathan, K., Cooperman, B.S., Lahti, R., Voet, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.272 (Depositor), 0.260 (DCC)
R-Value Work:
0.209 (Depositor), 0.200 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Refined Structure of Yeast Inorganic Pyrophosphatase and its K61R Mutant

Swaminathan, K., Cooperman, B.S., Lahti, R., Voet, D.

To be published.

Macromolecule Content

Total Structure Weight: 63.67 kDa
Atom Count: 4,811
Modelled Residue Count: 562
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INORGANIC PYROPHOSPHATASE	A, B	281	Saccharomyces cerevisiae	Mutation(s): 1 EC: 3.6.1.1
UniProt
Find proteins for P00817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00817 Go to UniProtKB: P00817
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00817
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.10 Å
R-Value Free: 0.272 (Depositor), 0.260 (DCC)
R-Value Work: 0.209 (Depositor), 0.200 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.05	α = 90
b = 92.52	β = 99.47
c = 51.58	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-04-08

Deposition Author(s):

Swaminathan, K.

Cooperman, B.S.

Revision History (Full details and data files)

Version 1.0: 1998-04-08
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-03
Changes: Database references, Derived calculations
Version 1.4: 2023-08-09
Changes: Refinement description
Version 1.5: 2024-05-22
Changes: Data collection

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.