3IMB | pdb_00003imb

Alternative binding mode of restriction endonuclease BcnI to cognate DNA

• PDB DOI: https://doi.org/10.2210/pdb3IMB/pdb
• NAKB: 3IMB

• Classification: HYDROLASE/DNA
• Organism(s): Brevibacillus centrosporus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-10 Released: 2010-08-11 
• Deposition Author(s): Sokolowska, M., Kaus-Drobek, M., Czapinska, H., Tamulaitis, G., Szczepanowski, R.H., Siksnys, V., Bochtler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

How BcnI and MvaI distinguish W from S

Sokolowska, M., Kaus-Drobek, M., Czapinska, H., Tamulaitis, G., Szczepanowski, R.H., Siksnys, V., Bochtler, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 131.24 kDa 
• Atom Count: 10,032 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,024 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
R.BcnI	A, B, C, D	238	Brevibacillus centrosporus	Mutation(s): 0  Gene Names: bcnIR
UniProt
Find proteins for Q8RNV8 (Brevibacillus centrosporus) Explore Q8RNV8  Go to UniProtKB:  Q8RNV8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'	E, G, I, K	9	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'	F, H, J, L	9	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.562	α = 90
b = 84.053	β = 100.09
c = 98.947	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Sokolowska, M., Kaus-Drobek, M., Czapinska, H., Tamulaitis, G., Szczepanowski, R.H., Siksnys, V., Bochtler, M.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description