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Yorodumi- PDB-3gqk: Crystal Structure of the Bacteriophage phi29 gene product 12 C-te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gqk | ||||||
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Title | Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment in complex with ATP | ||||||
Components | Preneck appendage protein | ||||||
Keywords | VIRAL PROTEIN / beta barrel | ||||||
Function / homology | Function and homology information virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xiang, Y. / Rossmann, M.G. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Authors: Xiang, Y. / Leiman, P.G. / Li, L. / Grimes, S. / Anderson, D.L. / Rossmann, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gqk.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gqk.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/3gqk ftp://data.pdbj.org/pub/pdb/validation_reports/gq/3gqk | HTTPS FTP |
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-Related structure data
Related structure data | 3gq7C 3gq8C 3gq9C 3gqaC 3gqhSC 3sucC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18014.301 Da / Num. of mol.: 1 / Fragment: D4, Residues 692-854 Source method: isolated from a genetically manipulated source Details: RESIDUES 692-854 EXPRESSED WITH A N-TERMIINAL HIS6 TAG Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 12, gene product 12 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: B3VMP8, UniProt: P20345*PLUS |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Sequence details | THESE MUTATIONS MIGHT BE AN ACCUMULATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis-Tris at pH 7.0, 20% PEG4K, 10%v/v MPD, 10mM MgCl2 and 10mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→26.95 Å / Num. obs: 7288 / % possible obs: 98.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.042 / Χ2: 1.35 / Net I/σ(I): 56.473 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GQH Resolution: 2.5→26.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 30.871 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.6 Å2 / Biso mean: 43.909 Å2 / Biso min: 26.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→26.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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