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Yorodumi- PDB-1ahs: CRYSTAL STRUCTURE OF THE TOP DOMAIN OF AFRICAN HORSE SICKNESS VIR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ahs | ||||||
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Title | CRYSTAL STRUCTURE OF THE TOP DOMAIN OF AFRICAN HORSE SICKNESS VIRUS VP7 | ||||||
Components | AFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7 | ||||||
Keywords | VIRAL PROTEIN / CORE PROTEIN / GLYCOPROTEIN / COAT PROTEIN (VIRAL) | ||||||
Function / homology | Function and homology information viral outer capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity Similarity search - Function | ||||||
Biological species | African horsesickness virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR/molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Stuart, D. / Gouet, P. | ||||||
Citation | Journal: J.Virol. / Year: 1996 Title: Crystal structure of the top domain of African horse sickness virus VP7: comparisons with bluetongue virus VP7. Authors: Basak, A.K. / Gouet, P. / Grimes, J. / Roy, P. / Stuart, D. #1: Journal: Nature / Year: 1995 Title: The Crystal Structure of Bluetongue Virus Vp7 Authors: Grimes, J. / Basak, A.K. / Roy, P. / Stuart, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ahs.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ahs.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ahs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ahs_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 1ahs_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 1ahs_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1ahs_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/1ahs ftp://data.pdbj.org/pub/pdb/validation_reports/ah/1ahs | HTTPS FTP |
-Related structure data
Related structure data | 1bvpS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13443.129 Da / Num. of mol.: 3 / Fragment: TOP DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) African horsesickness virus / Genus: Orbivirus / References: UniProt: P36325 #2: Water | ChemComp-HOH / | Compound details | THE TRIMERIC FRAGMENT OF AFRICAN HORSESICKNESS VIRUS CAN BE SUPERIMPOSED WITH THE 'TOP DOMAIN' OF ...THE TRIMERIC FRAGMENT OF AFRICAN HORSESICKN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.3→30 Å / Num. obs: 29456 / % possible obs: 91 % / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.089 |
-Processing
Software |
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Refinement | Method to determine structure: MIR/molecular replacement Starting model: 1BVP Resolution: 2.3→15 Å / σ(F): 0 Details: THE REFINEMENT WAS CARRIED OUT AGAINST A MERGE OF THE IN-HOUSE AND SYNCHROTRON DATA. THE THREE SUBUNITS WERE REFINED INDEPENDENTLY. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST A MERGE OF THE IN-HOUSE AND SYNCHROTRON DATA. THE THREE SUBUNITS WERE REFINED INDEPENDENTLY. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO MOLECULAR THREE-FOLD AXIS HAS AN UNLIKELY LOW TEMPERATURE FACTOR OF 2.00 A**2 AND MAY BE A CHLORIDE ION. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO MOLECULAR THREE-FOLD AXIS HAS AN UNLIKELY LOW TEMPERATURE FACTOR OF 2.00 A**2 AND MAY BE A CHLORIDE ION.
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |