+Open data
-Basic information
Entry | Database: PDB / ID: 1vsr | ||||||
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Title | VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI | ||||||
Components | PROTEIN (VSR ENDONUCLEASE) | ||||||
Keywords | HYDROLASE / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Tsutakawa, S.E. / Muto, T. / Jingami, H. / Kunishima, N. / Ariyoshi, M. / Kohda, D. / Nakagawa, M. / Morikawa, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vsr.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vsr.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vsr_validation.pdf.gz | 417.5 KB | Display | wwPDB validaton report |
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Full document | 1vsr_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 1vsr_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1vsr_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vsr ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vsr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Detector: IMAGE PLATE / Date: Nov 17, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method 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
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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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
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