3BAM | pdb_00003bam

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)

• PDB DOI: https://doi.org/10.2210/pdb3BAM/pdb
• NAKB: 3BAM

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


• Deposited: 1998-08-19 Released: 1999-01-13 
• Deposition Author(s): Viadiu, H., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.268 (Depositor) 
• R-Value Work: 
  0.226 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

The role of metals in catalysis by the restriction endonuclease BamHI.

Viadiu, H., Aggarwal, A.K.

(1998) Nat Struct Biol 5: 910-916

• PubMed: 9783752 
• DOI: https://doi.org/10.1038/2352
• Primary Citation Related Structures: 
  2BAM, 3BAM


• PubMed Abstract: 
  

  Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.59 kDa 
• Atom Count: 4,177 
• Modeled Residue Count: 438 
• Deposited Residue Count: 450 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)	D [auth A], E [auth B]	213	Bacillus amyloliquefaciens	Mutation(s): 0  EC: 3.1.21.4
UniProt
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')	A [auth C]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*G)-3')	B [auth D]	4	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')	C [auth E]	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	F [auth D], G [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.268 (Depositor) 
• R-Value Work:  0.226 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.4	α = 90
b = 79.6	β = 90
c = 67.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Viadiu, H., Aggarwal, A.K.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description