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- PDB-3fbl: Crystal structure of ORF132 of the archaeal virus Acidianus Filam... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fbl | ||||||
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Title | Crystal structure of ORF132 of the archaeal virus Acidianus Filamentous Virus 1 (AFV1) | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | STRUCTURAL PROTEIN / AFV1 / archaeal virus / extremophiles / lipothrixviridae / DNA-binding protein | ||||||
Function / homology | Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / helical viral capsid / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / DNA binding / Mainly Alpha / Major capsid protein 2![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Goulet, A. / Leulliot, N. / Prangishvili, D. / van Tilbeurgh, H. / Campanacci, V. / Cambillau, C. | ||||||
![]() | ![]() Title: Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage Authors: Goulet, A. / Blangy, S. / Redder, P. / Prangishvili, D. / Felisberto-Rodrigues, C. / Forterre, P. / Campanacci, V. / Cambillau, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.6 KB | Display | ![]() |
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PDB format | ![]() | 19.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.4 KB | Display | ![]() |
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Full document | ![]() | 412.4 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9168.595 Da / Num. of mol.: 1 / Fragment: ORF132 domain, residues 51-132 Source method: isolated from a genetically manipulated source Details: The protein expressed is a fusion with thioredoxin in N-terminal position. An hexahistidine-tag and a TEV protease cleavage site are inserted between thioredoxin and the protein of interest Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE PROTEIN USED FOR CRYSTALLIZATION IS THE FULL-LENGTH FORM, BUT THE PROTEIN IS DEGRADED IN ...THE PROTEIN USED FOR CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12% PEG 8000, 0.025 mM Na2HPO4/KH2PO4, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25.6 Å / Num. obs: 6349 / % possible obs: 100 % / Redundancy: 76 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 136.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 76 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 89 / Num. unique all: 902 / Rsym value: 0.066 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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