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Yorodumi- PDB-1cw0: CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cw0 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / MISMATCH / INTERCALATION / ZINC / HYDROLASE-DNA complex | ||||||
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 / Resolution: 2.3 Å | ||||||
Authors | Tsutakawa, S.E. / Jingami, H. / Morikawa, K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Authors: Tsutakawa, S.E. / Jingami, H. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cw0.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cw0.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cw0 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cw0 | HTTPS FTP |
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-Related structure data
Related structure data | 1vsrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 3 types, 3 molecules MNO
#1: DNA chain | Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 17914.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P09184, Hydrolases; Acting on ester bonds |
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-Non-polymers , 3 types, 209 molecules
#5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 / Details: pH 5.60, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.834 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→24.254 Å / Num. obs: 15166 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.316 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 22 Å / Num. obs: 15168 / % possible obs: 99.4 % / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.261 |
-Processing
Software |
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Refinement | Starting model: TRUNCATED VSR MODEL, 1VSR Resolution: 2.3→22 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.36 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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