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Yorodumi- PDB-4m95: d(ATCCGTTATAACGGAT)complexed with Moloney Murine Leukemia virus r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m95 | ||||||
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Title | d(ATCCGTTATAACGGAT)complexed with Moloney Murine Leukemia virus reverse transcriptase catalytic fragment | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Protein-DNA complex / Reverse transcriptase / DNA binding / DNA sequence / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus isolate Shinnick | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Singh, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. Authors: Singh, I. / Lian, Y. / Li, L. / Georgiadis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m95.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m95.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 4m95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m95_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
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Full document | 4m95_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 4m95_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4m95_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m95 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m95 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29347.754 Da / Num. of mol.: 1 / Fragment: UNP residues 683-937 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus isolate Shinnick Gene: gag-pol, Reverse transcriptase / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: P03355, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H | ||
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#2: DNA chain | Mass: 2401.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Polydeoxyribonucleotide | ||
#3: DNA chain | Mass: 2450.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Polydeoxyribonucleotide | ||
#4: Chemical | #5: 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: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2013 |
Radiation | Monochromator: Rosenbaum-Rock high resolution double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→26.7 Å / Num. all: 40829 / Num. obs: 40094 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→26.7 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.23 / σ(F): 0 / Phase error: 22.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.31 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→26.7 Å
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Refine LS restraints |
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