3KTY | pdb_00003kty

Crystal Structure of Probable Methyltransferase from Bordetella pertussis Tohama I

• PDB DOI: https://doi.org/10.2210/pdb3KTY/pdb

• Classification: TRANSFERASE
• Organism(s): Bordetella pertussis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-11-26 Released: 2009-12-08 
• Deposition Author(s): Kim, Y., Tesar, C., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structure of Probable Methyltransferase SpoU from Bordetella pertussis Tohama I

Kim, Y., Tesar, C., Keigher, L., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 56.37 kDa 
• Atom Count: 4,053 
• Modeled Residue Count: 510 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable methyltransferase	A, B, C	173	Bordetella pertussis	Mutation(s): 0  Gene Names: BP1901
UniProt
Find proteins for Q7VXA3 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VXA3  Go to UniProtKB:  Q7VXA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.48	α = 90
b = 69.514	β = 95.16
c = 174.802	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Kim, Y., Tesar, C., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary