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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.216 (Depositor), 0.226 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4HFS

This is version 1.3 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31803
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

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: 1.55 Å
R-Value Free: 0.216 (Depositor), 0.226 (DCC)
R-Value Work: 0.192 (Depositor), 0.201 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

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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.