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Yorodumi- PDB-2j6c: crystal structure of AFV3-109, a highly conserved protein from cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j6c | ||||||
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Title | crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses | ||||||
Components | AFV3-109 | ||||||
Keywords | VIRAL PROTEIN / VIRUS / ACIDIANUS / SULFOLOBUS / CRENARCHAEA | ||||||
Function / homology | Uncharacterised protein PF08960, DUF1874 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | ACIDIANUS FILAMENTOUS VIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Keller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Cortez, D. / Quevillon-Cheruel, S. / Van Tilbeurgh, H. | ||||||
Citation | Journal: Virol J. / Year: 2007 Title: Crystal Structure of Afv3-109, a Highly Conserved Protein from Crenarchaeal Viruses. Authors: Keller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Forterre, P. / Cortez, D. / Quevillon-Cheruel, S. / 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 | 2j6c.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j6c.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j6c_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 2j6c_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 2j6c_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2j6c_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/2j6c ftp://data.pdbj.org/pub/pdb/validation_reports/j6/2j6c | HTTPS FTP |
-Related structure data
-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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-Components
#1: Protein | Mass: 12337.417 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACIDIANUS FILAMENTOUS VIRUS 1 / Strain: 3 / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli) |
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#2: Chemical | ChemComp-GOL / |
#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: 2.8 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 8 / Details: 25% PEG 4000, 0.1M NAAC, 0.1M TRIS-HCL PH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 16423 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 59 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 3.9 / % possible all: 79.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→58.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.57 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.067 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→58.82 Å
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Refine LS restraints |
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