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- PDB-4rve: THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES ... -

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Basic information

Entry
Database: PDB / ID: 4rve
TitleTHE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS
Components
  • DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-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 / SYNCHROTRON / 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. / Wilso, 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: 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.
History
DepositionFeb 18, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
E: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
A: PROTEIN (ECO RV (E.C.3.1.21.4))
B: PROTEIN (ECO RV (E.C.3.1.21.4))
C: PROTEIN (ECO RV (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)94,8126
Polymers94,8126
Non-polymers00
Water41423
1
D: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
E: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-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)63,2084
Polymers63,2084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
C: PROTEIN (ECO RV (E.C.3.1.21.4))

F: DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
C: PROTEIN (ECO RV (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)63,2084
Polymers63,2084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)60.200, 78.400, 371.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES PRO A 73, PRO B 73, AND PRO C 73 ARE CIS PROLINES.

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Components

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


Mass: 3045.005 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Protein PROTEIN (ECO RV (E.C.3.1.21.4))


Mass: 28559.158 Da / Num. of mol.: 3
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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 400011
3NACL11
4WATER12
5NA PHOSPHATE12
6NACL12
Crystal grow
*PLUS
Details: Winkler, F.K., (1991) J.Mol.Biol., 217, 235. / PH range low: 6.9 / PH range high: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlenzyme 1drop
310-20 mMsodium potassium phosphate1reservoir
4250 mM1reservoirNaCl
52-6 mg/mloligonucleotide1reservoir
2ammonium sulfate1drop
61

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 15231
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 15988 / % possible obs: 90 % / Rmerge(I) obs: 0.073

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3→8 Å
Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND THE ATOMS AS FAR AS PRESENT ARE ENTERED WITH ZERO OCCUPANCIES AND B FACTORS OF 99.0. WITH THE EXCEPTION OF THE C-TERMINAL ...Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND THE ATOMS AS FAR AS PRESENT ARE ENTERED WITH ZERO OCCUPANCIES AND B FACTORS OF 99.0. WITH THE EXCEPTION OF THE C-TERMINAL RESIDUES 242-245, COORDINATES FOR THESE ILL-DEFINED 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 STRUCTURES PRESENT FOR THESE SEGMENTS IN THIS COORDINATE FILE ARE ONLY MEANT TO DELINEATE THE APPROXIMATE PATH OF THESE DISORDERED CHAIN SEGMENTS. IN THE FINAL TNT REFINEMENT ROUNDS THE CORRESPONDING ATOMS WERE INCLUDED WITH ZERO OCCUPANCIES TO MAINTAIN A REASONABLE STEREOCHEMISTRY. A 13 TO A 17 B 13 TO B 18 C 13 TO C 18 A 83 A 99 TO A 100 A 141 TO A 149 B 141 TO B 148 C 141 TO C 149 A 222 TO A 228 B 222 TO B 228 C 222 TO C 228 A 242 TO A 245 B 242 TO B 245 C 242 TO C 245 THE ATOMS OF A NUMBER OF SIDE CHAINS WITH POORLY DEFINED DENSITY ARE MARKED IN THE SAME WAY AND ARE: SUBUNIT A: GLU 57 B: LYS 67 C: GLU 57 LYS 98 ASN 70 LYS 85 LYS 85 LYS 98 LYS 98 GLU 99 GLU 99 ASN 100 GLU 101 LYS 102
RfactorNum. reflection
obs0.176 15231
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5961 606 0 23 6590
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: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.26

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