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Yorodumi- PDB-1m55: Catalytic domain of the Adeno Associated Virus type 5 Rep protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m55 | ||||||
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Title | Catalytic domain of the Adeno Associated Virus type 5 Rep protein | ||||||
Components | Rep protein | ||||||
Keywords | VIRAL PROTEIN / ENDONUCLEASE / REP / ROLLING CIRCLE REPLICATION / ADENO-ASSOCIATED VIRUS | ||||||
Function / homology | Function and homology information viral genome replication / DNA replication / host cell nucleus / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Adeno-associated virus - 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Hickman, A.B. / Ronning, D.R. / Kotin, R.M. / Dyda, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep. Authors: Hickman, A.B. / Ronning, D.R. / Kotin, R.M. / Dyda, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m55.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m55.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m55 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m55 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22776.982 Da / Num. of mol.: 2 / Fragment: Catalytic domain (Residues 1-197) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus - 5 / Genus: Dependovirus / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9YJC1 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, PEG 400, ZINC ACETATE, SODIUM CACODYLATE, TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 6, 2001 |
Radiation | Monochromator: Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 79390 / Num. obs: 79390 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.71 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.68 / Num. unique all: 4502 / Rsym value: 0.404 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 373647 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 95.9 % / Rmerge(I) obs: 0.404 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.46 Å / Rfactor Rfree error: 0.023
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.179 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.36 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.279 / Rfactor Rwork: 0.261 |