3H5Q | pdb_00003h5q

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3H5Q/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-22 Released: 2009-05-26
Deposition Author(s): Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.204 (Depositor), 0.201 (DCC)
R-Value Work:
0.166 (Depositor), 0.171 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 47.85 kDa
Atom Count: 3,729
Modeled Residue Count: 436
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine-nucleoside phosphorylase	A	436	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1 Gene Names: pdp, pyn, SACOL2128 EC: 2.4.2.2
UniProt
Find proteins for Q5HE64 (Staphylococcus aureus (strain COL)) Explore Q5HE64 Go to UniProtKB: Q5HE64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HE64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THM Query on THM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.204 (Depositor), 0.201 (DCC)
R-Value Work: 0.166 (Depositor), 0.171 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.591	α = 90
b = 40.885	β = 97.19
c = 105.578	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2021-10-13
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2022-04-13
Changes: Database references, Structure summary
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary