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Yorodumi- PDB-2vqc: Structure of a DNA binding winged-helix protein, F-112, from Sulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqc | |||||||||
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Title | Structure of a DNA binding winged-helix protein, F-112, from Sulfolobus Spindle-shaped Virus 1. | |||||||||
Components | HYPOTHETICAL 13.2 KDA PROTEIN | |||||||||
Keywords | DNA BINDING PROTEIN / SSV / WINGED-HELIX / CRENARCHAEAL / DNA-BINDING PROTEIN / THERMOPHILIC PROTEIN / SULFOLOBUS SPINDLE VIRUS | |||||||||
Function / homology | F-112 protein-like / Sulfolobus spindle-shape virus 1 F-112 protein-like / F-112 protein / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Protein F-112 Function and homology information | |||||||||
Biological species | SULFOLOBUS VIRUS-LIKE PARTICLE SSV1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | |||||||||
Authors | Menon, S.K. / Kraft, P. / Corn, G.J. / Wiedenheft, B. / Young, M.J. / Lawrence, C.M. | |||||||||
Citation | Journal: Virology / Year: 2008 Title: Cysteine Usage in Sulfolobus Spindle-Shaped Virus 1 and Extension to Hyperthermophilic Viruses in General. Authors: Menon, S.K. / Maaty, W.S. / Corn, G.J. / Kwok, S.C. / Eilers, B.J. / Kraft, P. / Gillitzer, E. / Young, M.J. / Bothner, B. / 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 | 2vqc.cif.gz | 25.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqc.ent.gz | 20.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqc ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqc | HTTPS FTP |
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-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: 14191.573 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS VIRUS-LIKE PARTICLE SSV1 / Plasmid: PEXP14- SSV1 F112 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20220 |
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#2: 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: 1.8 Å3/Da / Density % sol: 31.9 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: HANGING DROP VAPOR DIFFUSION IN 0.1M MES (PH 6.0). QIUCK SOAK IN ML CONTAINING 25% GLYCEROL AS A CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.891940, 0.979180, 0.979320 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2005 / Details: MIRROR | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→30 Å / Num. obs: 4411 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6 | ||||||||||||
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 12.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.3→25.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.361 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 AND 74-112 ARE DISORDERED
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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: 23.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.53 Å
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Refine LS restraints |
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