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Yorodumi- PDB-1hrh: CRYSTAL STRUCTURE OF THE RIBONUCLEASE H DOMAIN OF HIV-1 REVERSE T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hrh | ||||||
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Title | CRYSTAL STRUCTURE OF THE RIBONUCLEASE H DOMAIN OF HIV-1 REVERSE TRANSCRIPTASE | ||||||
Components | RIBONUCLEASE H | ||||||
Keywords | HYDROLASE(ENDORIBONUCLEASE) | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Davies /II, J.F. / Matthews, D.A. | ||||||
Citation | Journal: Science / Year: 1991 Title: Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Authors: Davies 2nd., J.F. / Hostomska, Z. / Hostomsky, Z. / Jordan, S.R. / Matthews, D.A. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Proteolytic Release and Crystallization of the Rnase H Domain of Human Immunodeficiency Virus Type I Reverse Transcriptase Authors: Hostomska, Z. / Matthews, D.A. / Davies /II, J.F. / Nodes, B.R. / Hostomsky, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hrh.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hrh.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/1hrh ftp://data.pdbj.org/pub/pdb/validation_reports/hr/1hrh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.3698, -0.78761, 0.49286), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. | |
-Components
#1: Protein | Mass: 15031.130 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P03366 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 13047 / % possible obs: 93.1 % / Num. measured all: 32084 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 90.4 % / Num. unique obs: 2521 / Num. measured obs: 3359 / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 1.6 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.2 / Highest resolution: 2.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.4 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR/PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / Total num. of bins used: 6 / Rfactor obs: 0.232 |