+Open data
-Basic information
Entry | Database: PDB / ID: 2j85 | |||||||||
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Title | B116 of Sulfolobus turreted icosahedral virus (STIV) | |||||||||
Components | STIV B116 | |||||||||
Keywords | VIRAL PROTEIN / ARCHAEAL VIRUS / CRENARCHAEAL VIRUS / B116 / STIV / ARCHAEA / SULFOLOBUS / CRENARCHAEA / SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / HYPOTHETICAL PROTEIN | |||||||||
Function / homology | Uncharacterised protein PF08960, DUF1874 / STIV B116-like / STIV B116-like superfamily / STIV B116-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | |||||||||
Biological species | SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å | |||||||||
Authors | Larson, E.T. / Reiter, D. / Young, M.J. / Lawrence, C.M. | |||||||||
Citation | Journal: Virology / Year: 2007 Title: A New DNA Binding Protein Highly Conserved in Diverse Crenarchaeal Viruses Authors: Larson, E.T. / Eilers, B.J. / Reiter, D. / Ortmann, A.C. / Young, M.J. / Lawrence, C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j85.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j85.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 2j85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j85_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2j85_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 2j85_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2j85_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j85 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j85 | HTTPS FTP |
-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
#1: Protein | Mass: 14409.745 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / Strain: ISOLATE YNPRC179 Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN INYELLOWSTONE NATIONAL PARK ...Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN INYELLOWSTONE NATIONAL PARK (RICE, ET AL. PNAS. MAY 18, 2004 VOL. 101 NO. 20. PP. 7716-7720.) Plasmid: PEXP14-STIVB116 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q6Q0K9 #2: Water | ChemComp-HOH / | Sequence details | C-TERMINUS 6XHIS TAG WAS ADDED DURING CLONING. | |
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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: 3.3 Å3/Da / Density % sol: 62.4 % Description: DATA WERE COLLECTED DURING RAPIDATA 2004 COURSE AT NSLS. |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 6.5 MG/ML PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN 0.1 M TRIS-HCL (PH 8.0), 1.95 M NH4H2PO4 AT 17 DEGREES C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2004 / Details: MIRRORS |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 14911 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.39→29.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.526 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUP SELECTIONS WERE MADE WITH THE AID OF TLS MOTION DETERMINATION SERVER. PAINTER AND MERRITT. 2005. ACTA CRYST D61, 465-471. CHAIN A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUP SELECTIONS WERE MADE WITH THE AID OF TLS MOTION DETERMINATION SERVER. PAINTER AND MERRITT. 2005. ACTA CRYST D61, 465-471. CHAIN A AND CHAIN B TOGETHER MAKE UP THE BIOLOGICAL MOLECULE.
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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: 28.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→29.81 Å
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