4FIB | pdb_00004fib

Crystal structure of the ydhK protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR518A.

PDB DOI: https://doi.org/10.2210/pdb4FIB/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-08 Released: 2012-06-20
Deposition Author(s): Vorobiev, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Maglaqui, M., Owens, L.A., Cunningham, K., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.255 (Depositor), 0.243 (DCC)
R-Value Work:
0.204 (Depositor), 0.195 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the ydhK protein from Bacillus subtilis.

Vorobiev, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Maglaqui, M., Owens, L.A., Cunningham, K., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 43.82 kDa
Atom Count: 2,997
Modeled Residue Count: 372
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ydhK	A, B, C	129	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: BSU05790, ydhK
UniProt
Find proteins for O05503 (Bacillus subtilis (strain 168)) Explore O05503 Go to UniProtKB: O05503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05503
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.255 (Depositor), 0.243 (DCC)
R-Value Work: 0.204 (Depositor), 0.195 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.861	α = 90
b = 69.493	β = 113.94
c = 61.487	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary