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

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Basic information

Entry
Database: PDB / ID: 1eop
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 / Resolution: 2.6 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

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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)64,7524
Polymers64,7524
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.1, 66.1, 299.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
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: 3685.441 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 / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 4000, 0.1 M acetate, 0.2 M tartrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1acetate11
2tartarate11
3PEG 400011
4PEG 400012
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
30.1 Macetate1reservoir
40.2 MNa/K-tartrate1reservoir
510 %PEG40001reservoir
2DNA1drop1.5-fold molar excess

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12971
22971
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATEMar 9, 1997
RIGAKU RAXIS II2IMAGE PLATEMar 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 18023 / Num. obs: 18023 / % possible obs: 78 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 4
Reflection
*PLUS
Num. measured all: 96208
Reflection shell
*PLUS
% possible obs: 50 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.6→4.8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: X-Plor
RfactorNum. reflection% reflectionSelection details
Rfree0.302 677 3.8 %random
Rwork0.181 ---
all0.187 18023 --
obs0.187 18023 78 %-
Refinement stepCycle: LAST / Resolution: 2.6→4.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 446 0 70 4359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.8

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