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- PDB-1bam: STRUCTURE OF RESTRICTION ENDONUCLEASE BAMHI PHASED AT 1.95 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 1bam
TitleSTRUCTURE OF RESTRICTION ENDONUCLEASE BAMHI PHASED AT 1.95 ANGSTROMS RESOLUTION BY MAD ANALYSIS
ComponentsENDONUCLEASE BamH I
KeywordsENDONUCLEASE
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, BamHI / Restriction endonuclease BamHI / Restriction endonuclease, type II, BamHI/BglIII/BstY / Restriction Endonuclease - #20 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme BamHI
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsAggarwal, A.K. / Newman, M.
Citation
Journal: Structure / Year: 1994
Title: Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis.
Authors: Newman, M. / Strzelecka, T. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
#1: Journal: Nature / Year: 1994
Title: Structure of Restriction Endonuclease BamHI and its Relationship to EcoRI
Authors: Newman, M. / Strzelecka, T. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionDec 28, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 650HELIX HELIX A6 IS A MIXTURE OF TYPE 1 AND TYPE 5. PRO 164 IN THE MIDDLE OF THE HELIX KINKS IT. ...HELIX HELIX A6 IS A MIXTURE OF TYPE 1 AND TYPE 5. PRO 164 IN THE MIDDLE OF THE HELIX KINKS IT. RESIDUES 159 - 162 FORM AN ALPHA HELIX. RESIDUE 163 - 165 AND 166 - 169 FORM A 3/10 HELIX.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDONUCLEASE BamH I


Theoretical massNumber of molelcules
Total (without water)24,6021
Polymers24,6021
Non-polymers00
Water2,090116
1
A: ENDONUCLEASE BamH I

A: ENDONUCLEASE BamH I


Theoretical massNumber of molelcules
Total (without water)49,2052
Polymers49,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)76.400, 46.000, 69.400
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 39

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Components

#1: Protein ENDONUCLEASE BamH I


Mass: 24602.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria)
References: UniProt: P23940, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
20.5 M1dropKCl
320 mM1dropKPO4
41 mMDTT1drop
515 %glycerol1drop
612 %PEG80001drop
70.25 M1dropKCl
80.2 %1dropNaN3
9crushed crystal1drop
1012 %PEG80001reservoir
1120 mM1reservoirKPO4
1210 %glycerol1reservoir
130.5 M1reservoirKCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 14335 / % possible obs: 86.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 1.95 Å
Refinement stepCycle: LAST / Highest resolution: 1.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 0 116 1735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19 / Lowest resolution: 10 Å / σ(F): 2 / Rfactor Rfree: 0.297
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.6

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