2PSB | pdb_00002psb

Crystal structure of YerB protein from Bacillus subtilis. NorthEast Structural Genomics target SR586

PDB DOI: https://doi.org/10.2210/pdb2PSB/pdb

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

Deposited: 2007-05-04 Released: 2007-05-15
Deposition Author(s): Seetharaman, J., Chen, Y., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.269 (Depositor), 0.275 (DCC)
R-Value Work:
0.218 (Depositor), 0.226 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of YerB protein from Bacillus subtilis.

Seetharaman, J., Chen, Y., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 36.05 kDa
Atom Count: 2,432
Modeled Residue Count: 290
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YerB protein	A	320	Bacillus subtilis	Mutation(s): 3 Gene Names: yerB, BSU06570
UniProt
Find proteins for O34968 (Bacillus subtilis (strain 168)) Explore O34968 Go to UniProtKB: O34968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34968
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269 (Depositor), 0.275 (DCC)
R-Value Work: 0.218 (Depositor), 0.226 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.216	α = 90
b = 43.216	β = 90
c = 128.835	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-05-15
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: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary