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- PDB-1nnd: Arginine 116 is Essential for Nucleic Acid Recognition by the Fin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nnd | ||||||
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Title | Arginine 116 is Essential for Nucleic Acid Recognition by the Fingers Domain of Moloney Murine Leukemia Virus Reverse Transcriptase | ||||||
![]() | Reverse Transcriptase | ||||||
![]() | TRANSFERASE / Nucleic Acid Binding / MMLV Reverse Transcriptase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Crowther, R.L. / Remeta, D.P. / Minetti, C.A. / Das, D. / Montano, S.P. / Georgiadis, M.M. | ||||||
![]() | ![]() Title: Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase Authors: Crowther, R.L. / Remeta, D.P. / Minetti, C.A. / Das, D. / Montano, S.P. / Georgiadis, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.6 KB | Display | ![]() |
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Full document | ![]() | 434.7 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qaiS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28848.170 Da / Num. of mol.: 1 / Fragment: MMLV Reverse Transcriptase / Mutation: R116A Source method: isolated from a genetically manipulated source Details: part of Pol polyprotein / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, Magnesium Chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2000 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 13028 / Num. obs: 12449 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 83.9 |
Reflection | *PLUS Num. obs: 12471 / % possible obs: 95.8 % / Num. measured all: 58875 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / % possible obs: 83.9 % / Rmerge(I) obs: 0.13 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QAI MOLECULE A Resolution: 2.3→32.84 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9656 Å2 / ksol: 0.342102 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→32.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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