2DLB | pdb_00002dlb

X-ray Crystal Structure of Protein yopT from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR412

• PDB DOI: https://doi.org/10.2210/pdb2DLB/pdb

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


• Deposited: 2006-04-18 Released: 2006-04-25 
• Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Ho, C.-K., Cunningham, K., Janjua, H., Conover, K., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.173 (Depositor), 0.167 (DCC) 

Literature

X-ray structure of hypothetical protein from Bacillus subtilis O34498 at the resolution of 1.2A. NESG target SR412

Kuzin, A.P., Chen, Y., Seetharaman, J., Ho, C.-K., Cunningham, K., Janjua, H., Conover, K., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.5 kDa 
• Atom Count: 1,294 
• Modeled Residue Count: 140 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
yopT	A, B	80	Bacillus subtilis	Mutation(s): 2
UniProt
Find proteins for O34498 (Bacillus subtilis (strain 168)) Explore O34498  Go to UniProtKB:  O34498

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.173 (Depositor), 0.167 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.347	α = 90
b = 76.116	β = 90
c = 78.385	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
ADSC	data collection
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Ho, C.-K., Cunningham, K., Janjua, H., Conover, K., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary