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- PDB-2rve: THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES ... -

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Basic information

Entry
Database: PDB / ID: 2rve
TitleTHE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS
Components
  • DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
  • PROTEIN (ECO RV (E.C.3.1.21.4))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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 / Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWinkler, 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.
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: 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.
History
DepositionMar 19, 1991Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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(*CP*GP*AP*GP*CP*TP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
E: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
A: PROTEIN (ECO RV (E.C.3.1.21.4))
B: PROTEIN (ECO RV (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)66,8296
Polymers66,8296
Non-polymers00
Water1,22568
1
C: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
A: PROTEIN (ECO RV (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)33,4143
Polymers33,4143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
B: PROTEIN (ECO RV (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)33,4143
Polymers33,4143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 79.600, 66.400
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2427.605 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein PROTEIN (ECO RV (E.C.3.1.21.4))


Mass: 28559.158 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 400011
3NACLSodium chloride11
4WATER12
5MES12
6NACLSodium chloride12
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 6.9 / PH range high: 6.4 / Details: Winkler, F.K., (1991) J.Mol.Biol., 217, 235.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlenzyme 1drop
2ammonium sulfate1drop
310-20 mMsodium potassium phosphate1reservoir
4250 mM1reservoirNaCl
52-6 mg/mloligonucleotide1reservoir
61

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 12143
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 17027 / % possible obs: 99 % / Num. measured all: 32155 / Rmerge(I) obs: 0.047

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3→6 Å / σ(F): 1
Details: THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY BUT HAVE NOT BEEN EXCLUDED FROM THIS ENTRY: A CHAIN: ASP 19, SER 35, LYS 67, LYS 85, LYS 98, LYS 197, LYS 203, ASN 231 B ...Details: THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY BUT HAVE NOT BEEN EXCLUDED FROM THIS ENTRY: A CHAIN: ASP 19, SER 35, LYS 67, LYS 85, LYS 98, LYS 197, LYS 203, ASN 231 B CHAIN: GLU 27, LYS 85, LYS 164
RfactorNum. reflection
obs0.178 11127
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 644 0 68 4240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.74
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / σ(F): 1 / Rfactor obs: 0.178 / Num. reflection obs: 11127
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d1.75
X-RAY DIFFRACTIONt_angle_deg1.75

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