4RQB

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group)

PDB DOI: https://doi.org/10.2210/pdb4RQB/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus USA300_TCH1516
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-31 Released: 2014-11-26
Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.221
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group)

Ghosh, A., Ahmed, A., Bhoshle, R., Seidel, R., Stead, M., Toro, R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 43.17 kDa
Atom Count: 3,006
Modelled Residue Count: 362
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A, B	186	Staphylococcus aureus subsp. aureus USA300_TCH1516	Mutation(s): 0 Gene Names: hpt EC: 2.4.2.8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	C [auth A], E [auth A], F [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	G [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
UNL Query on UNL Download Ideal Coordinates CCD File	D [auth A], L [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.221
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.244	α = 90
b = 109.244	β = 90
c = 100.79	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Ghosh, A.

Almo, S.C.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection

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4RQB

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group)

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group)

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)