4I3E | pdb_00004i3e

Crystal structure of Staphylococcal IMPase - I complexed with products.

PDB DOI: https://doi.org/10.2210/pdb4I3E/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus MSSA476
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-26 Released: 2013-12-18
Deposition Author(s): Bhattacharyya, S., Dutta, A., Dutta, D., Das, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.260 (Depositor), 0.229 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4I3E

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

Literature

Crystal structure of Staphylococcal IMPase - I complexed with products.

Bhattacharyya, S., Dutta, A., Dutta, D., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 62.95 kDa
Atom Count: 4,300
Modeled Residue Count: 521
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol monophosphatase family protein	A, B	271	Staphylococcus aureus subsp. aureus MSSA476	Mutation(s): 0 Gene Names: SAS2203 EC: 3.1.3.25

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] F [auth A] G [auth A] I [auth B] K [auth B] C [auth A], F [auth A], G [auth A], I [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.260 (Depositor), 0.229 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.327	α = 90
b = 62.51	β = 90
c = 140.925	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Bhattacharyya, S.

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.