1TO0 | pdb_00001to0

X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1TO0/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-06-11 Released: 2004-07-20 
• Deposition Author(s): Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Shastry, R., Ma, L.-C., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis

Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Shastry, R., Ma, L.-C., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 155.65 kDa 
• Atom Count: 9,527 
• Modelled Residue Count: 1,174 
• Deposited Residue Count: 1,336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical UPF0247 protein yyda	A, B, C, D, E, F, G, H	167	Bacillus subtilis	Mutation(s): 6  Gene Names: YYDA, BSU40230 EC: 2.1.1.177
UniProt
Find proteins for Q45601 (Bacillus subtilis (strain 168)) Explore Q45601  Go to UniProtKB:  Q45601

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	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:  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.691	α = 90
b = 70.553	β = 95.16
c = 100.488	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-20 
Deposition Author(s): Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Shastry, R., Ma, L.-C., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2004-07-20
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary