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- PDB-1rve: THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES ... -

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Basic information

Entry
Database: PDB / ID: 1rve
TitleTHE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS
ComponentsENDONUCLEASE EcoR V
KeywordsENDONUCLEASE
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
Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWinkler, F.K.
Citation
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.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1992
Title: Structure and Function of Restriction Endonucleases
Authors: Winkler, F.K.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of Complexes of EcoRV Endonuclease with Cognate and Non-Cognate DNA Fragments
Authors: Winkler, F.K. / D'Arcy, A. / Bloecker, H. / Frank, R. / Van Boom, J.H.
#3: Journal: J.Biol.Chem. / Year: 1985
Title: Purification and Crystallization of the EcoRV Restriction Endonuclease
Authors: D'Arcy, A. / Brown, R.S. / Zabeau, M. / Van Resandt, R.W. / Winkler, F.K.
History
DepositionFeb 24, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
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
A: ENDONUCLEASE EcoR V
B: ENDONUCLEASE EcoR V


Theoretical massNumber of molelcules
Total (without water)57,3812
Polymers57,3812
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-21 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.200, 71.700, 130.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO A 73 AND PRO B 73 ARE CIS PROLINES.
2: THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY (THEY WERE INCLUDED IN THE REFINEMENT AND ARE ENTERED WITH UNIT OCCUPANCIES): A CHAIN: GLN 68, GLN 69, ASN 70, LYS 245 B CHAIN: LYS 161

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Components

#1: Protein ENDONUCLEASE EcoR V


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 7.8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 mg/mlprotein1drop
221-24 %(w/v)PEG40001drop
30.1-0.15 M1dropNaCl
410 %PEG40001reservoir
50.18 M1reservoirNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 16509 / Num. measured all: 86437 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 0
Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND ARE ENTERED WITH ZERO OCCUPANCIES. THE CORRESPONDING B FACTORS ARE MEANINGLESS. THE COORDINATES OF THE ATOMS OF THESE SEGMENTS ...Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND ARE ENTERED WITH ZERO OCCUPANCIES. THE CORRESPONDING B FACTORS ARE MEANINGLESS. THE COORDINATES OF THE ATOMS OF THESE SEGMENTS HAVE BEEN PRODUCED THROUGH THE INITIAL MOLECULAR DYNAMICS RUNS STARTING WITH ARBITRARY CONFORMATIONS AND UNIT OCCUPANCIES. THE DENSITY IN THESE REGIONS IS MOSTLY WEAK AND FRAGMENTED. THE RESIDUES HAVE BEEN LEFT IN THIS COORDINATE FILE JUST TO DELINEATE THE APPROXIMATE PATH OF THE CHAIN IN THESE REGIONS. THEY WERE INCLUDED WITH ZERO OCCUPANCIES IN TNT REFINEMENT TO MAINTAIN REASONABLE STEREOCHEMISTRY. A 13 TO A 17 B 13 TO B 19 A 142 TO A 148 B 142 TO B 148 A 183 TO A 187 B 183 TO B 187 A 221 TO A 228 B 221 TO B 228 THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY (THEY WERE INCLUDED IN THE REFINEMENT AND ARE ENTERED WITH UNIT OCCUPANCIES): A CHAIN: GLN 68, GLN 69, ASN 70, LYS 245 B CHAIN: LYS 161
RfactorNum. reflection
Rwork0.185 -
obs0.185 15963
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 0 49 4095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.07
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection all: 15963 / σ(F): 0 / Rfactor all: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.07

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