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- PDB-1bhm: RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1bhm
TitleRESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA
Components
  • DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
  • PROTEIN (BAMHI (E.C.3.1.21.4))
KeywordsHYDROLASE/DNA / HYDROLASE / COMPLEX (ENDONUCLEASE-DNA) / NUCLEASE / HYDROLASE-DNA COMPLEX
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
DNA / DNA (> 10) / Type II restriction enzyme BamHI
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsAggarwal, A.K. / Newman, M.
CitationJournal: Science / Year: 1995
Title: Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding.
Authors: Newman, M. / Strzelecka, T. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionJul 12, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 12, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
A: PROTEIN (BAMHI (E.C.3.1.21.4))
B: PROTEIN (BAMHI (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)56,5274
Polymers56,5274
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.800, 81.900, 68.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO BAMHI MONOMERS (CHAINS A AND B) BOUND TO A PALINDROMIC 12 BASE PAIR DNA COMPLEX.

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Components

#1: DNA chain DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (BAMHI (E.C.3.1.21.4)) / R. BAMHI


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


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2GLYCEROL11
3PEG 800011
4K PHOSPHATE11
5DTT11
6KCL11
7BIS-TRIS-PROPANE_HCL11
8EDTAEthylenediaminetetraacetic acid11
9NACLSodium chloride11
10WATER12
11PEG 800012
12GLYCEROL12
13KCL12
Crystal grow
*PLUS
Details: Strzelecka, T., (1994) J. Mol. Biol, 239, 430.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.23 mMBamHI1drop
20.46 mMDNA1drop
33 %glycerol1drop
46.1 mM1dropKPO4
50.3 mM1drop
60.15 M1dropKCl
73.9 mMTris-HCl1drop
80.4 mM1drop
93.9 mM1dropNaCl
1012 %PEG80001drop
112 %glycerol1drop
1212 %PEG80001reservoir
130.15 M1reservoirKCl
145 %glycerol1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 30078 / % possible obs: 94.2 %
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 94.2 % / Num. measured all: 103881 / Rmerge(I) obs: 0.118

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: THE 3' ADENINE RESIDUE ON ONE OF THE DNA STRANDS IS DISORDERED.
RfactorNum. reflection
obs0.189 28405
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 465 0 215 3888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.8

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