4HFS | pdb_00004hfs

Crystal structure of an uncharacterized protein (yncM) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4HFS/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-05 Released: 2012-12-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of an uncharacterized protein (yncM) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 46.59 kDa 
• Atom Count: 3,838 
• Modeled Residue Count: 406 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YncM	A, B	212	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU17690, NP_389652.1, yncM
UniProt
Find proteins for O31803 (Bacillus subtilis (strain 168)) Explore O31803  Go to UniProtKB:  O31803

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HFS

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43	α = 90
b = 42.71	β = 97.62
c = 119.71	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Data collection, Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary