Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.53 kDa 
• Atom Count: 3886 
• Residue Count: 429 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1BHM

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA

• DOI: 10.2210/pdb1BHM/pdb
• NDB: PDE020

• Classification: HYDROLASE/DNA
• Organism(s): Bacillus amyloliquefaciens
• Mutation(s): No 


• Deposited: 1995-07-12 Released: 1995-07-12 
• Deposition Author(s): Aggarwal, A.K., Newman, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.189 

Literature

Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding.

Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I., Aggarwal, A.K.

(1995) Science 269: 656-663

• PubMed: 7624794 
• DOI: 10.1126/science.7624794
• Primary Citation of Related Structures:  
  1BHM


• PubMed Abstract: 
  

The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BAMHI (E.C.3.1.21.4))	A, B	213	Bacillus amyloliquefaciens	Mutation(s): 0  Gene Names: bamHIR EC: 3.1.21.4
Find proteins for P23940 (Bacillus amyloliquefaciens) Explore P23940  Go to UniProtKB:  P23940

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')	C, D	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.8	α = 90
b = 81.9	β = 90
c = 68.8	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-07-12 
• Released Date: 1995-07-12 
Deposition Author(s): Aggarwal, A.K., Newman, M.

Revision History 

• Version 1.0: 1995-07-12
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance