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Yorodumi- PDB-6bo3: Structure Determination of A223, a turret protein in Sulfolobus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bo3 | ||||||
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Title | Structure Determination of A223, a turret protein in Sulfolobus turreted icosahedral virus, using an iterative hybrid approach | ||||||
Components | Uncharacterized protein | ||||||
Keywords | VIRAL PROTEIN / A223 / STIV / C381 / twin / twinning / 3j31 / 4IL7 | ||||||
Function / homology | Jelly Rolls - #1300 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Sulfolobus turreted icosahedral virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Sendamarai, A.K. / Veesler, D. / Fu, C.Y. / Marceau, C. / Larson, E.T. / Johnson, J.E. / Lawrence, C.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: STRUCTURAL CHARACTERIZATION OF A223, A STRUCTURAL PROTEIN FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS (STIV) Authors: Sendamarai, A.K. / 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 | 6bo3.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bo3.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/6bo3 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bo3 | HTTPS FTP |
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-Related structure data
Related structure data | 3j31S S: Starting model for refinement |
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Similar structure data |
-Links
-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 / End auth comp-ID: ILE / End label comp-ID: ILE
NCS oper:
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-Components
#1: Protein | Mass: 25286.529 Da / Num. of mol.: 2 / Mutation: L208M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus turreted icosahedral virus 1 Gene: A223 / Plasmid: pDEST14 / Details (production host): Invitrogen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus (DE3) RIL / References: UniProt: Q6Q0L4 #2: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density meas: 0.225 Mg/m3 / Density % sol: 53.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Crystals of A223-L208M were grown by hanging drop vapour diffusion using 2 micro-L of the protein solution and 2 micro-L in 0.1 M tri-sodium citrate dihydrate pH 5.6 and 35% t-butanol. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.82653 Å | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2009 Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1 | |||||||||||||||
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.82653 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.82→50 Å / Num. obs: 47436 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.9 | |||||||||||||||
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Num. unique obs: 4662 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3J31 Resolution: 1.83→20.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.216 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.02 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.73 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→20.85 Å
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Refine LS restraints |
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