1TO9 | pdb_00001to9

Crystal structure of THI-4 protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1TO9/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-06-14 Released: 2004-08-10 
• Deposition Author(s): Rajan, S.S., Shuvalova, L., Yang, X., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal structure of THI-4 protein from Bacillus subtilis

Rajan, S.S., Shuvalova, L., Yang, X., Hussar, C., Collart, F., Anderson, W.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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.35 kDa 
• Atom Count: 3,758 
• Modeled Residue Count: 448 
• Deposited Residue Count: 520 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THI-4 protein	A	260	Bacillus subtilis	Mutation(s): 6  Gene Names: TENA, BSU11650 EC: 3.5.99.2
UniProt
Find proteins for P25052 (Bacillus subtilis (strain 168)) Explore P25052  Go to UniProtKB:  P25052

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THI-4 protein	B	260	Bacillus subtilis	Mutation(s): 6  Gene Names: TENA, BSU11650 EC: 3.5.99.2
UniProt
Find proteins for P25052 (Bacillus subtilis (strain 168)) Explore P25052  Go to UniProtKB:  P25052

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HMH	C [auth A], D [auth B]	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE C6 H9 N3 O VUTBELPREDJDDH-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
CSD	B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.38	α = 90
b = 58.38	β = 90
c = 296.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Rajan, S.S., Shuvalova, L., Yang, X., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2014-11-19
  Changes: Non-polymer description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary