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Yorodumi- PDB-2wb6: Crystal structure of AFV1-102, a protein from the Acidianus Filam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wb6 | ||||||
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Title | Crystal structure of AFV1-102, a protein from the Acidianus Filamentous Virus 1 | ||||||
Components | AFV1-102 | ||||||
Keywords | VIRAL PROTEIN / ARCHAEAL VIRUS | ||||||
Function / homology | Aspartate Aminotransferase, domain 1 - #90 / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein ORF102 Function and homology information | ||||||
Biological species | ACIDIANUS FILAMENTOUS VIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Keller, J. / Leulliot, N. / Collinet, B. / Campanacci, V. / Cambillau, C. / Pranghisvilli, D. / van Tilbeurgh, H. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Crystal Structure of Afv1-102, a Protein from the Acidianus Filamentous Virus 1. Authors: Keller, J. / Leulliot, N. / Collinet, B. / Campanacci, V. / Cambillau, C. / Pranghisvilli, D. / Van Tilbeurgh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wb6.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wb6.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 2wb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wb6_validation.pdf.gz | 422 KB | Display | wwPDB validaton report |
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Full document | 2wb6_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 2wb6_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2wb6_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wb6 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wb6 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 15049.633 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACIDIANUS FILAMENTOUS VIRUS 1 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q70LC3 | ||
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#2: Chemical | #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: 2.1 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 1.5-2M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54.47 Å / Num. obs: 10006 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 34.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 38 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 0.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.95→54.47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.236 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.031 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→54.47 Å
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Refine LS restraints |
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