2GUJ | pdb_00002guj

Three dimensional structure of the protein P54332 from Bacillus Subtilis. Northeast Structural Genomics Consortium target sr353.

PDB DOI: https://doi.org/10.2210/pdb2GUJ/pdb

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

Deposited: 2006-04-30 Released: 2006-05-23
Deposition Author(s): Kuzin, A.P., Zhou, W., Seetharaman, J., Cunningham, K., Janjua, H., Konover, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.285 (Depositor), 0.302 (DCC)
R-Value Work:
0.253 (Depositor), 0.269 (DCC)
R-Value Observed:
0.253 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Three dimensional structure of the protein P54332 from Bacillus Subtilis. Northeast Structural Genomics Consortium target sr353.

Kuzin, A.P., Zhou, W., Seetharaman, J., Cunningham, K., Janjua, H., Konover, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 35.45 kDa
Atom Count: 2,116
Modeled Residue Count: 270
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-like element PBSX protein xkdM	A, B	155	Bacillus subtilis	Mutation(s): 6 Gene Names: xkdM
UniProt
Find proteins for P54332 (Bacillus subtilis (strain 168)) Explore P54332 Go to UniProtKB: P54332
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54332
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: 3.00 Å
R-Value Free: 0.285 (Depositor), 0.302 (DCC)
R-Value Work: 0.253 (Depositor), 0.269 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.255	α = 90
b = 84.255	β = 90
c = 46.694	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-05-23
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: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary