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- PDB-1az4: ECORV ENDONUCLEASE, UNLIGANDED, FORM B, T93A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1az4
TitleECORV ENDONUCLEASE, UNLIGANDED, FORM B, T93A MUTANT
ComponentsECORV ENDONUCLEASE
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPerona, J. / Martin, A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.
Authors: Perona, J.J. / Martin, A.M.
#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
DepositionNov 24, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2012Group: Database references
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECORV ENDONUCLEASE
B: ECORV ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)57,0582
Polymers57,0582
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-20 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 121.700, 59.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ECORV ENDONUCLEASE


Mass: 28529.131 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.8 mg/mlprotein1drop
28 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
DetectorDate: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Biso Wilson estimate: 38.9 Å2
Reflection
*PLUS
Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.337 -10 %
Rwork0.225 --
obs0.225 16989 75 %
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 0 42 3218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.83
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
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: 2.4→2.5 Å /
Rfactor% reflection
Rfree0.404 -
Rwork0.315 -
obs-56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor obs: 0.315

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