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- PDB-1esg: RESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA. -

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Basic information

Entry
Database: PDB / ID: 1esg
TitleRESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA.
Components
  • DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*AP*TP*TP*CP*A)-3')
  • TYPE II RESTRICTION ENZYME BAMHI
KeywordsHYDROLASE/DNA / Non-specific DNA-protein complex. / 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 / Type II restriction enzyme BamHI
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsViadiu, H. / Aggarwal, A.K.
Citation
Journal: Mol.Cell / Year: 2000
Title: Structure of BamHI bound to nonspecific DNA: a model for DNA sliding.
Authors: Viadiu, H. / Aggarwal, A.K.
#1: Journal: To be Published / Year: 2000
Title: A step towards understanding protein-DNA specificity: crystallization of the restriction endonuclease BamHI with a non-specific DNA
Authors: Viadiu, H. / Kucera, R. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionApr 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 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*GP*GP*AP*TP*TP*CP*A)-3')
D: DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3')
A: TYPE II RESTRICTION ENZYME BAMHI
B: TYPE II RESTRICTION ENZYME BAMHI


Theoretical massNumber of molelcules
Total (without water)54,0574
Polymers54,0574
Non-polymers00
Water10,431579
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.8, 91.1, 66.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsA protein dimer with a double stranded DNA.

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Components

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


Mass: 2441.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphoramite synthesis
#2: DNA chain DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3')


Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphoramite synthesis
#3: Protein TYPE II RESTRICTION ENZYME BAMHI / E.C.3.1.21.4 / ENDONUCLEASE BAMHI / R.BAMHI / TYPE II SITE-SPECIFIC DEOXYRIBONUCLEASE


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


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 30% MPD, 10 mM sodium acetate (pH 4.8), 5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2CaCl211
3MPD11
4MPD12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
116-20 %MPD1
25 mM1CaCl2
310 mMsodium acetate1
41

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
31101
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.5418
SYNCHROTRONCHESS A120.91
SYNCHROTRONCHESS A130.91
Detector
TypeIDDetectorDate
RIGAKU RAXIS1IMAGE PLATEJul 15, 1998
MACSCIENCE2CCDAug 15, 1998
MACSCIENCE3CCDAug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.911
ReflectionResolution: 1.9→10 Å / Num. all: 53008 / Num. obs: 53008 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.284 / Num. unique all: 5404 / % possible all: 85.2
Reflection shell
*PLUS
% possible obs: 85.2 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: protein: Engh & Huber, DNA: Parkinson et al.
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2574 5 %Random
Rwork0.1907 ---
all-55112 --
obs-51166 92.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 322 0 572 4308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.48
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.1 Å2

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