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Yorodumi- PDB-1uut: The Nuclease Domain of Adeno-Associated Virus Rep Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uut | ||||||
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Title | The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the RBE' Stemloop of the Viral Inverted Terminal Repeat | ||||||
Components |
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Keywords | HYDROLASE/DNA / NUCLEASE-COMPLEX / VIRAL PROTEIN / NUCLEASE / REPLICATION / PROTEIN-DNA / STEMLOOP / HELICASE / HYDROLASE-DNA complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dyda, F. / Hickman, A.B. / Ronning, D.R. / Perez, Z.N. / Kotin, R.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: The Nuclease Domain of Adeno-Associated Virus Rep Coordinates Replication Initiation Using Two Distinct DNA Recognition Interfaces Authors: Hickman, A.B. / Ronning, D.R. / Perez, Z.N. / Kotin, R.M. / Dyda, F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uut.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uut.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uut ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uut | HTTPS FTP |
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-Related structure data
Related structure data | 1rz9C 1m55S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.7938, -0.5824, 0.1755), Vector: Details | THE NUCLEASE DOMAIN OF THE REP PROTEIN HAS NO EVIDENCESHOWING OLIGOMERIZATION, AND MAY THEREFORE BE CONSIDEREDTO BE A MONOMER. IN THIS ENTRY, SINCE THE PROTEIN IS INCOMPLEX WITH DNA FROM THE INVERTED TERMINAL REPEATSEUENCES OF AAV-5 , THE COMPLEX IS ANNOTATED AS A DIMERICASSOCIATION . | |
-Components
#1: Protein | Mass: 22776.982 Da / Num. of mol.: 2 / Fragment: NUCLEASE DOMAIN, RESIDUES 1-197 Source method: isolated from a genetically manipulated source Details: ALL RESIDUES ARE DELETED AFTER S197 / Source: (gene. exp.) ADENO-ASSOCIATED VIRUS 5 / Strain: SEROTYPE 5 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YJC1 #2: DNA chain | Mass: 4575.970 Da / Num. of mol.: 2 / Fragment: RBE STEMLOOP, RESIDUES 1-15 / Source method: obtained synthetically / Source: (synth.) ADENO-ASSOCIATED VIRUS 5 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: 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: 2.77 Å3/Da / Density % sol: 55.64 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 2003 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: MULTILAYER MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 38009 / % possible obs: 90 % / Redundancy: 4.2 % / Biso Wilson estimate: 25.02 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 3.8 / % possible all: 57 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 89.7 % / Num. measured all: 158265 / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M55 Resolution: 2→30 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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