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- PDB-1bua: STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPEC... -

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Basic information

Entry
Database: PDB / ID: 1bua
TitleSTRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE
Components
  • DNA (5'-D(*AP*AP*AP*GP*AP*CP*IP*TP*CP*TP*T)-3')
  • ENDONUCLEASE ECORV
Keywordshydrolase/DNA / ENDONUCLEASE ECORV (E.C.3.1.21.4)-DNA COMPLEX / 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 / OTHER / Resolution: 2.15 Å
AuthorsPerona, J.J. / Martin, A.M.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Metal Ion Mediated Substrate-Assisted Catalysis in Type II Restriction Endonucleases
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
DepositionSep 3, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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(*AP*AP*AP*GP*AP*CP*IP*TP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*AP*GP*AP*CP*IP*TP*CP*TP*T)-3')
A: ENDONUCLEASE ECORV
B: ENDONUCLEASE ECORV


Theoretical massNumber of molelcules
Total (without water)63,8034
Polymers63,8034
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)50.300, 64.200, 49.400
Angle α, β, γ (deg.)109.30, 108.30, 96.30
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 3342.209 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein ENDONUCLEASE ECORV / 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, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.2 mg/mlprotein1drop
21.8 mg/mlDNA1drop
35-10 %PEG40001reservoir
450 mMHEPES1reservoirpH7.5
5150 mM1reservoirNaCl
625 mM5'-AAAGACITCTT1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 37374 / % possible obs: 86 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.056
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 83222
Reflection shell
*PLUS
% possible obs: 75.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB 1AZ0

1az0


Resolution: 2.15→6 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: THE AMIMO ACID SIDE CHAINS LISTED IN REMARK 470 APPEAR TO BE PARTIALLY OR COMPLETELY DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -10 %RANDOM
Rwork0.2 ---
obs-22040 75 %-
Displacement parametersBiso mean: 26.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 444 0 236 4307
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_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PR0TOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNA0TOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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