2EUC | pdb_00002euc

Crystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324

PDB DOI: https://doi.org/10.2210/pdb2EUC/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-10-28 Released: 2005-11-08
Deposition Author(s): Benach, J., Abashidze, M., Jayaraman, S., Janjua, H., Cooper, B., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.328 (Depositor), 0.332 (DCC)
R-Value Work:
0.274 (Depositor), 0.277 (DCC)
R-Value Observed:
0.274 (Depositor)

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

Literature

Crystal structure of YfmB from bacillus subtilis NESG TARGET SR324.

Benach, J., Abashidze, M., Jayaraman, S., Rong, X., Acton, T.B., Montelione, G.T., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 30.62 kDa
Atom Count: 1,960
Modeled Residue Count: 216
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yfmB	A, B	130	Bacillus subtilis	Mutation(s): 4 Gene Names: yfmB
UniProt
Find proteins for O34626 (Bacillus subtilis (strain 168)) Explore O34626 Go to UniProtKB: O34626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34626
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.50 Å
R-Value Free: 0.328 (Depositor), 0.332 (DCC)
R-Value Work: 0.274 (Depositor), 0.277 (DCC)
R-Value Observed: 0.274 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.543	α = 90
b = 67.637	β = 90
c = 78.015	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-11-08

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-11-08
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.