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Yorodumi- PDB-1d0e: CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d0e | ||||||
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Title | CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / POLYMERASE / REVERSE TRANSCRIPTASE / MOLONEY MURINE LEUKEMIA VIRUS / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...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 / RNA-directed DNA polymerase / viral genome integration into host DNA / 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 / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain Authors: Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M. #1: Journal: Protein Sci. / Year: 1998 Title: Cloning, expression and purification of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase: Crystallization of nucleic acid complexes Authors: Sun, D. / Jessen, S. / Liu, C. / Liu, X. / Najmudin, S. / Georgiadis, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d0e.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d0e.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d0e ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d0e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3339.195 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 29347.754 Da / Num. of mol.: 2 Fragment: N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: MMLV-RT / Plasmid: PRT 107-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase |
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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: 2.29 Å3/Da / Density % sol: 46.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 4000,0.1M NH4CL,0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: used to seeding, Sun, D., (1998) Protein Sci., 7, 1575. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→500 Å / Num. all: 11540 / Num. obs: 11540 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 5.95 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.314 / % possible all: 92.2 |
Reflection | *PLUS Num. measured all: 35570 |
Reflection shell | *PLUS % possible obs: 92.2 % |
-Processing
Software |
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Refinement | Resolution: 3→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 31.1 Å2
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Refinement step | Cycle: LAST / Resolution: 3→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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