3FYM | pdb_00003fym

The 1A structure of YmfM, a putative DNA-binding membrane protein from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3FYM/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-22 Released: 2010-02-09
Deposition Author(s): Xu, L., Sedelnikova, S.E., Baker, P.J., Rice, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.140 (Depositor)
R-Value Work:
0.110 (Depositor), 0.125 (DCC)
R-Value Observed:
0.110 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The 1A structure of YmfM, a putative DNA-binding membrane protein from Staphylococcus aureus

Xu, L., Sedelnikova, S.E., Baker, P.J., Rice, D.W.

To be published.

Macromolecule Content

Total Structure Weight: 15.2 kDa
Atom Count: 846
Modeled Residue Count: 82
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	130	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0
UniProt
Find proteins for A0A0H3JZ73 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JZ73 Go to UniProtKB: A0A0H3JZ73
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3JZ73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.140 (Depositor)
R-Value Work: 0.110 (Depositor), 0.125 (DCC)
R-Value Observed: 0.110 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.456	α = 90
b = 45.456	β = 90
c = 72.903	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing
SHELXL	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Sedelnikova, S.E.

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 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.