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Yorodumi- PDB-2rsp: STRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rsp | ||||||
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Title | STRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS REFINED AT 2 ANGSTROMS RESOLUTION | ||||||
Components | RSV PROTEASE | ||||||
Keywords | HYDROLASE(ASPARTYL PROTEINASE) | ||||||
Function / homology | Function and homology information host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Wlodawer, A. / Miller, M. / Jaskolski, M. | ||||||
Citation | Journal: Biochemistry / Year: 1990 Title: Structure of the aspartic protease from Rous sarcoma retrovirus refined at 2-A resolution. Authors: Jaskolski, M. / Miller, M. / Rao, J.K. / Leis, J. / Wlodawer, A. #1: Journal: Nature / Year: 1989 Title: Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family Authors: Miller, M. / Jaskolski, M. / Rao, J.K.M. / Leis, J. / Wlodawer, A. | ||||||
History |
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Remark 700 | SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET (SHEET *INT* BELOW). SHEETS MA AND MB ARE EACH DISRUPTED BY BULGES AT RESIDUES ASP 78 IN STRAND 2 AND ARG 93 IN STRAND 3. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rsp.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rsp.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/2rsp ftp://data.pdbj.org/pub/pdb/validation_reports/rs/2rsp | 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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Components on special symmetry positions |
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Details | THE ACTIVE ENZYME IS A DIMER COMPOSED OF TWO RSV PR MOLECULES. THIS DIMER COMPRISES THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE MOLECULES IN THIS DIMER ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS WHICH IS NEARLY COINCIDENT WITH THE (2 1 -3) CRYSTAL DIRECTION. CHAIN IDENTIFIERS *A* AND *B* HAVE BEEN ASSIGNED TO THE TWO MOLECULES PRESENTED IN THIS ENTRY. |
-Components
#1: Protein | Mass: 13625.862 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P03322 #2: Water | ChemComp-HOH / | Compound details | THE CATALYTIC SITE IS FORMED BY TWO ASP-SER-GLY LOOPS, ONE FORM EACH SUBUNIT, CONNECTED BY AN ...THE CATALYTIC SITE IS FORMED BY TWO ASP-SER-GLY LOOPS, ONE FORM EACH SUBUNIT, CONNECTED BY AN INTRICATE SYSTEM OF HYDROGEN BONDS. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.78 % |
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Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion |
Components of the solutions | *PLUS Common name: ammonium sulfate |
-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 20613 / % possible obs: 86 % / Observed criterion σ(I): 1.5 / Num. measured all: 95106 / Rmerge(I) obs: 0.069 |
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-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→10 Å Details: THE SG ATOMS OF CYS A 113 AND CYS B 113 HAVE BEEN REFINED IN TWO ALTERNATE POSITIONS WITH AN OCCUPANCY OF 0.5 FOR EACH POSITION.
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 17609 / Rfactor obs: 0.144 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 2.2 Å |