4EBG | pdb_00004ebg

Crystal structure of a DUF4467 family protein (SAV0303) from Staphylococcus aureus subsp. aureus Mu50 at 1.35 A resolution

PDB DOI: https://doi.org/10.2210/pdb4EBG/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-23 Released: 2012-05-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.167 (Depositor), 0.190 (DCC)
R-Value Work:
0.136 (Depositor), 0.160 (DCC)
R-Value Observed:
0.138 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a hypothetical protein (SAV0303) from Staphylococcus aureus subsp. aureus Mu50 at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 24.6 kDa
Atom Count: 2,098
Modeled Residue Count: 196
Deposited Residue Count: 202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	101	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: SAV0303
UniProt
Find proteins for A0A0H3JX79 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JX79 Go to UniProtKB: A0A0H3JX79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3JX79
Sequence Annotations Expand
Reference Sequence

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 D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 1.20 Å
R-Value Free: 0.167 (Depositor), 0.190 (DCC)
R-Value Work: 0.136 (Depositor), 0.160 (DCC)
R-Value Observed: 0.138 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34EBG

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.244	α = 86.06
b = 35.058	β = 79.66
c = 50.073	γ = 71.6

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary

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.