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Yorodumi- PDB-3g26: Crystal structure of the C-terminal domain of the Rous Sarcoma Vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g26 | ||||||
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Title | Crystal structure of the C-terminal domain of the Rous Sarcoma Virus capsid protein: Mutant A184C | ||||||
Components | Gag polyprotein | ||||||
Keywords | VIRAL PROTEIN / ALPHA-HELICAL BUNDLE / CAPSID PROTEIN / VIRION / RETROVIRUS | ||||||
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 / aspartic-type endopeptidase activity / nucleic acid binding / structural constituent of virion / host cell plasma membrane / proteolysis ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / nucleic acid binding / structural constituent of virion / host cell plasma membrane / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Kingston, R.L. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly Authors: Bailey, G.D. / Hyun, J.K. / Mitra, A.K. / Kingston, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g26.cif.gz | 30.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g26.ent.gz | 19.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g26_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 3g26_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 3g26_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 3g26_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/3g26 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/3g26 | HTTPS FTP |
-Related structure data
Related structure data | 3g0vC 3g1gC 3g1iC 3g21C 3g28SC 3g29C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8506.701 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 389-465 / Mutation: A184C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C strain / Gene: gag / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) References: UniProt: P03322, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
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#2: Chemical | ChemComp-MLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.7 Details: 0.1M Malic acid/KOH, pH3.7, 1.4 M Malonic acid/KOH, pH3.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.77337 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77337 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28 Å / Num. all: 10622 / Num. obs: 10622 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1006 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G28 Resolution: 1.55→27.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.294 / SU ML: 0.048 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: There is a disulfide bond between CYS 184 and its symmetry equivalent in the crystal.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.404 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→27.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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