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Open data
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Basic information
Entry | Database: PDB / ID: 1tbx | ||||||
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Title | Crystal structure of SSV1 F-93 | ||||||
![]() | Hypothetical 11.0 kDa protein | ||||||
![]() | VIRAL PROTEIN / Sulfolobus Spindle Virus / Winged Helix / F-93 / fusellovirus | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / Protein F-93![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kraft, P. / Oeckinghaus, A. / Kummel, D. / Gauss, G.H. / Wiedenheft, B. / Young, M. / Lawrence, C.M. | ||||||
![]() | ![]() Title: Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein. Authors: Kraft, P. / Oeckinghaus, A. / Kummel, D. / Gauss, G.H. / Gilmore, J. / Wiedenheft, B. / Young, M. / Lawrence, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.4 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.3 KB | Display | ![]() |
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Full document | ![]() | 430 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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Details | The biological assembly is thought to correspond to the dimer of the asymmetric unit. |
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Components
#1: Protein | Mass: 11905.413 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 3.25 M NaCl, 120 mM HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→20 Å / Num. obs: 7936 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 9.24 % / Rsym value: 0.05 / Net I/σ(I): 41 | ||||||||||||
Reflection shell | Resolution: 2.7→2.81 Å / Rsym value: 0.167 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.457 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→14 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.771 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 79.7916 Å / Origin y: 60.6764 Å / Origin z: 35.9355 Å
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Refinement TLS group |
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