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Yorodumi- PDB-1rdh: CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdh | ||||||
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Title | CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAIN SHOW STRUCTURAL FEATURES THAT DISTINGUISH IT FROM THE INACTIVE FORM | ||||||
Components | HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN) | ||||||
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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Finzel, B.C. / Chattopadhyay, D. / Einspahr, H.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form. Authors: Chattopadhyay, D. / Finzel, B.C. / Munson, S.H. / Evans, D.B. / Sharma, S.K. / Strakalaitus, N.A. / Brunner, D.P. / Eckenrode, F.M. / Dauter, Z. / Betzel, C. / Einspahr, H.M. #1: Journal: Science / Year: 1991 Title: Crystal Structure of the Ribonuclease H Domain of HIV-1 Reverse Transcriptase Authors: Davies II, J.F. / Hostomska, Z. / Hostomsky, Z. / Jordan, S.R. / Matthews, D.A. #2: Journal: J.Biol.Chem. / Year: 1991 Title: A Recombinant Ribonuclease H Domain of HIV-1 Reverse Transcriptase that is Enzymatically Active Authors: Evans, D.B. / Brawn, K. / Deibel Junior, M.R. / Tarpley, W.G. / Sharma, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdh.cif.gz | 21 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdh.ent.gz | 10 KB | Display | PDB format |
PDBx/mmJSON format | 1rdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdh ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdh | 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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2 |
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Unit cell |
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Details | THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THEY HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE RESIDUE NUMBERING IS BASED ON THE REVERSE TRANSCRIPTASE SEQUENCE. |
-Components
#1: Protein | Mass: 16196.366 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase Sequence details | THIS RECOMBINANT VERSION OF THE HIV-1 RNASE H DOMAIN WAS PREPARED WITH AN N-TERMINAL SEQUENCE TO ...THIS RECOMBINAN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.23 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.2 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 8145 / % possible obs: 95 % / Num. measured all: 19985 / Rmerge(I) obs: 0.072 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→20 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |