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- PDB-2b0d: EcoRV Restriction Endonuclease/GAATTC/Ca2+ -

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Basic information

Entry
Database: PDB / ID: 2b0d
TitleEcoRV Restriction Endonuclease/GAATTC/Ca2+
Components
  • 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'
  • Type II restriction enzyme EcoRV
KeywordsHYDROLASE/DNA / protein-nucleic acid recognition / indirect readout / restriction enzyme / substrate specificity / noncognate / 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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHiller, D.A. / Rodriguez, A.M. / Perona, J.J.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC
Authors: Hiller, D.A. / Rodriguez, A.M. / Perona, J.J.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
Authors: Martin, A.M. / Sam, M.D. / Reich, N.O. / Perona, J.J.
#2: Journal: Biochemistry / Year: 2003
Title: Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence
Authors: Hiller, D.A. / Fogg, J.M. / Martin, A.M. / Beechem, J.M. / Reich, N.O. / Perona, J.J.
#3: Journal: Biochemistry / Year: 2004
Title: DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites
Authors: Horton, N.C. / Perona, J.J.
History
DepositionSep 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'
D: 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'
A: Type II restriction enzyme EcoRV
B: Type II restriction enzyme EcoRV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1736
Polymers64,0934
Non-polymers802
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.000, 48.400, 63.600
Angle α, β, γ (deg.)97.20, 109.00, 106.60
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'


Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Type II restriction enzyme EcoRV / 3.1.21.4 / Endonuclease EcoRV / R.EcoRV


Mass: 28690.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoRVR / Plasmid: pBSRV / Production host: Escherichia coli (E. coli) / Strain (production host): mm294
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4K, Hepes, NaCl, CaCl2, Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2Hepes11
3NaCl11
4CaCl211
5H2O11
6PEG 4K12
7Hepes12
8NaCl12
9CaCl212
10Glycerol12
11H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 30291 / % possible obs: 89.1 % / Net I/σ(I): 8
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 3.1 / % possible all: 82.3

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Processing

Software
NameVersionClassificationNB
X-PLORrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
CNSrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→6 Å /
RfactorNum. reflection
Rfree0.302 -
Rwork0.22 -
obs-30291
Displacement parametersBiso mean: 19.952 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 446 2 262 4488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.92

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