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- PDB-1bgb: ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA -

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Basic information

Entry
Database: PDB / ID: 1bgb
TitleECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA
Components
  • DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
  • ECORV ENDONUCLEASE
KeywordsHYDROLASE/DNA / COMPLEX (ENDONUCLEASE-DNA) / 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 / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsPerona, J. / Horton, N.C.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
Authors: Horton, N.C. / Perona, J.J.
#1: 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.
#2: 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.
History
DepositionMay 28, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
D: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')
A: ECORV ENDONUCLEASE
B: ECORV ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)63,7874
Polymers63,7874
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.400, 50.200, 64.100
Angle α, β, γ (deg.)96.00, 109.00, 108.00
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 3334.186 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein ECORV ENDONUCLEASE / EC 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, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 43.63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALLIZED FROM 15% PEG 4K, 100 MM IMIDAZOLE, (PH 6.5), 150 MM NACL., VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1IMIDAZOLE11
2NACL11
3PEG 400011
4PEG 400012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.17 mMEcoRV1drop
20.34 mMDNA1drop
315 %PEG40001reservoir
4100 mMimidazol1reservoirpH6.5
5150 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25665 / % possible obs: 85 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.091 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.28 / % possible all: 71

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1512 10 %RANDOM
Rwork0.184 ---
obs0.184 31018 88 %-
Displacement parametersBiso mean: 27.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 426 0 236 4264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
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→2.2 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 112 10 %
Rwork0.257 1211 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNA0TOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42

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