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- PDB-1rv5: COMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT) -

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Basic information

Entry
Database: PDB / ID: 1rv5
TitleCOMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT)
Components
  • 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
  • ECORV ENDONUCLEASE
KeywordsHYDROLASE/DNA / ENDONUCLEASE ECORV-DNA 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 / 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: 2.1 Å
AuthorsHorton, N.C. / Perona, J.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT).
Authors: Horton, N.C. / Perona, J.J.
#1: Journal: Embo J. / Year: 1993
Title: The Crystal Structure of EcoRV Endonuclease and of its Complexes with Cognate and Non-Cognate DNA Fragments
Authors: Winkler, F.K. / Banner, D.W. / Oefner, C. / Tsernoglou, D. / Brown, R.S. / Heathman, S.P. / Bryan, R.K. / Martin, P.D. / Petratos, K. / Wilson, K.S.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1992
Title: Structure and Function of Restriction Endonucleases
Authors: Winkler, F.K.
History
DepositionJun 1, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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: 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
D: 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
A: ECORV ENDONUCLEASE
B: ECORV ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)63,8314
Polymers63,8314
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 50.400, 63.900
Angle α, β, γ (deg.)96.40, 109.20, 108.50
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: DNA chain 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3' / COGNATE SEQUENCE


Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein ECORV ENDONUCLEASE


Mass: 28559.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlEcoRV11
21.0 mg/mlDNA11
35 mM11NaF
40.3 mM11AlCl3
530 mM11MgCl2
6100 mMHEPES12pH7.5
7150 mM12NaCl
810-15 %PEG400012

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29460 / % possible obs: 80 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.078
Reflection
*PLUS
Num. measured all: 128913

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 1RVA

1rva


Resolution: 2.1→6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.272 488 2 %RANDOM
Rwork0.193 ---
obs0.193 27705 80 %-
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 478 0 492 5619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.483
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
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.272 39 1.55 %
Rwork0.304 2007 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PR0TOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNA0TOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.622
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.483

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