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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.140 (Depositor) 
• R-Value Work: 
  0.110 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.110 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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), 0.120 (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

Entry History 

Deposition Data

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

Revision History  

• 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