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- PDB-1vsr: VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1vsr
TitleVERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (VSR ENDONUCLEASE)
KeywordsHYDROLASE / ENDONUCLEASE / DNA REPAIR / MISMATCH RECOGNITION
Function / homology
Function and homology information


T/G mismatch-specific endonuclease activity / mismatch repair / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
DNA mismatch endonuclease VSR / DNA mismatch endonuclease Vsr / Endonuclease; Chain A / VSR Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA mismatch endonuclease Vsr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsTsutakawa, S.E. / Muto, T. / Jingami, H. / Kunishima, N. / Ariyoshi, M. / Kohda, D. / Nakagawa, M. / Morikawa, K.
CitationJournal: Mol.Cell / Year: 1999
Title: Crystallographic and functional studies of very short patch repair endonuclease.
Authors: Tsutakawa, S.E. / Muto, T. / Kawate, T. / Jingami, H. / Kunishima, N. / Ariyoshi, M. / Kohda, D. / Nakagawa, M. / Morikawa, K.
History
DepositionFeb 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PROTEIN (VSR ENDONUCLEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8502
Polymers15,7851
Non-polymers651
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.020, 54.240, 73.520
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 PROTEIN (VSR ENDONUCLEASE) / PATCH REPAIR PROTEIN / DNA MISMATCH ENDONUCLEASE


Mass: 15785.019 Da / Num. of mol.: 1 / Fragment: FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Description: PCR / Gene: VSR / Plasmid: PLMVSR1 / Species (production host): Escherichia coli / Gene (production host): VSR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P09184, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.2 Å3/Da / Density % sol: 44.38 %
Crystal growpH: 6.5
Details: CRYSTALLIZATION CONDITIONS: ROOM TEMPERATURE BATCH, 75 MM SODIUM PHOSPHATE PH 6.5, 150 MM NACL, 2 MM DTT, 10% PEG 4K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
175 mMsodium phosphate11
2150 mM11NaCl
310 %PEG400011
410 mg/mlprotein11

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Nov 17, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 12869 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.177 / % possible all: 91.4
Reflection
*PLUS
Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: USED ROUNDS OF XPLOR AND REFMAC FOR REFINEMENT XPLOR-2 SIGMA CUTOFF, 6-1.8 A REFMAC-NO SIGMA CUTOFF, 20-1.8 A, BULK SOLVENT CORRECTION BOND LENGTHS (A) : 0.004 BOND ANGLES (DEGREES) : 2.1
RfactorNum. reflection% reflectionSelection details
Rfree0.216 637 5 %RANDOM
Rwork0.1962 ---
obs-12206 94.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 1 63 1161
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_deg2.1

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