1M38

Structure of Inorganic Pyrophosphatase

PDB DOI: https://doi.org/10.2210/pdb1M38/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2002-06-27 Released: 2003-01-28
Deposition Author(s): Kuranova, I.P., Polyakov, K.M., Levdikov, V.M., Smirnova, E.A., Hohne, W.E., Lamzin, V.S., Meijers, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.241 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Kuranova, I.P., Polyakov, K.M., Smirnova, E.A., Hohne, W.E., Lamzin, V.S., Meijers, R.

(2003) Crystallogr Rep 48: 953-958

Macromolecule Content

Total Structure Weight: 65.22 kDa
Atom Count: 5,234
Modelled Residue Count: 564
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
INORGANIC PYROPHOSPHATASE	A, B	287	Saccharomyces cerevisiae	Mutation(s): 0 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.241 (Depositor), 0.230 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.69	α = 90
b = 93.23	β = 99.74
c = 69.84	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
BLANC	model building
REFMAC	refinement
CCP4	data scaling
BLANC	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-01-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-01-28
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations