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- PDB-1eoo: ECORV BOUND TO COGNATE DNA -

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Basic information

Entry
Database: PDB / ID: 1eoo
TitleECORV BOUND TO COGNATE DNA
Components
  • DNA (5'-D(*GP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*C)-3')
  • TYPE II RESTRICTION ENZYME ECORV
Keywordshydrolase/DNA / protein-DNA recognition / induced fit / endonuclease / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
Restriction endonuclease, type II, EcoRV / Restriction endonuclease, type II, EcoRV, Proteobacteria / Restriction endonuclease EcoRV / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.16 Å
AuthorsHorton, N.C. / Perona, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystallographic snapshots along a protein-induced DNA-bending pathway.
Authors: Horton, N.C. / Perona, J.J.
History
DepositionMar 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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(*GP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*C)-3')
D: DNA (5'-D(*GP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*C)-3')
A: TYPE II RESTRICTION ENZYME ECORV
B: TYPE II RESTRICTION ENZYME ECORV


Theoretical massNumber of molelcules
Total (without water)64,7044
Polymers64,7044
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.6, 120.4, 182.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe biological assembly is a dimer composed of chains A and B / The biological assembly is a duplex composed of chains C and D

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Components

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


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein TYPE II RESTRICTION ENZYME ECORV / E.C.3.1.21.4 / ENDONUCLEASE ECORV / R.ECORV


Mass: 28690.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5 M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2(NH4)2SO412
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlEcoRV1drop
31.5 Mammonium sulfate1reservoir
2DNA1drop1.5-fold molar excess

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979
DetectorType: OTHER / Detector: CCD / Date: Apr 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→20 Å / Num. all: 21638 / Num. obs: 21638 / % possible obs: 82 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.1
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.315 / Num. unique all: 1285 / % possible all: 81.5
Reflection
*PLUS
Num. measured all: 50635
Reflection shell
*PLUS
% possible obs: 81.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementResolution: 2.16→4.8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: X-Plor
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1620 5 %random
Rwork0.231 ---
all0.2285 32743 --
obs0.2285 32743 80.3 %-
Refinement stepCycle: LAST / Resolution: 2.16→4.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 486 0 293 4667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.1

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