[English] 日本語
Yorodumi- PDB-4m94: d(ATCCGTTATAACGGAT) complexed with Moloney Murine Leukemia virus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m94 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | d(ATCCGTTATAACGGAT) complexed with Moloney Murine Leukemia virus reverse transcriptase catalytic fragment | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSFERASE/DNA / Protein-DNA complex / Reverse transcriptase / DNA binding / Spore photoproduct / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4m94.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4m94.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 4m94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m94 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m94 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||
---|---|---|---|
#2: DNA chain | Mass: 2403.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 2450.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others) | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% 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: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jul 27, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→33.73 Å / Num. all: 21193 / Num. obs: 19858 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Biso Wilson estimate: 19.05 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→33.73 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 21.04 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.61 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.54 Å2
| ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→33.73 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell |
|