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- PDB-3gqa: Crystal Structure of the Bacteriophage phi29 gene product 12 N-te... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gqa | ||||||
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Title | Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with cobalt ions | ||||||
![]() | Preneck appendage protein | ||||||
![]() | VIRAL PROTEIN / beta helix | ||||||
Function / homology | ![]() virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, Y. / Rossmann, M.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.6 KB | Display | ![]() |
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PDB format | ![]() | 99.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gq7SC ![]() 3gq8C ![]() 3gq9C ![]() 3gqhC ![]() 3gqkC ![]() 3sucC S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 64410.914 Da / Num. of mol.: 1 / Fragment: D1*D2D3, Residues 89-691 Source method: isolated from a genetically manipulated source Details: RESIDUES 89-854 EXPRESSED WITH A N-TERMIINAL HIS6 TAG Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Sequence details | THESE MUTATIONS MIGHT BE AN ACCUMULATE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the ...Details: 100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the apo-crystals in a mother liquid containing 10mM cobalt ions, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.1→43.88 Å / Num. obs: 53528 / % possible obs: 99.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.099 / Χ2: 1.843 / Net I/σ(I): 31.667 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GQ7 Resolution: 2.1→43.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.317 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.145 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.63 Å2 / Biso mean: 29.128 Å2 / Biso min: 16.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.157 Å / Total num. of bins used: 20
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