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- PDB-3dpb: Crystal structure of the complex of the Caf1M chaperone with the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dpb | ||||||
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Title | Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand | ||||||
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![]() | CHAPERONE/STRUCTURAL PROTEIN / DONOR STRAND COMPLEMENTATION / FIMBRIAE / ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() capsule / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fooks, L.J. / Yu, X. / Moslehi-Mohebi, E. / Tischenko, V. / Knight, S.D. / MacIntyre, S. / Zavialov, A.V. | ||||||
![]() | ![]() Title: Hydrophobicity and rigidity of binding segments enable CAF1M chaperone to act as assembly catalyst Authors: Fooks, L.J. / Yu, X. / Moslehi-Mohebi, E. / Tischenko, V. / Knight, S.D. / MacIntyre, S. / Zavialov, A.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.4 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dosC ![]() 3dsnC ![]() 1z9sS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 26329.012 Da / Num. of mol.: 1 / Fragment: UNP residues 24 to 258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 15617.234 Da / Num. of mol.: 2 / Fragment: UNP residues22 to 170 / Mutation: Ala9Val, Ala11Val, Leu13Val Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 16-17% PEG 8000 in 0.1 M Na cacodylate and 0.2 M Ca acetate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2006 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→40 Å / Num. obs: 24702 / % possible obs: 82.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible all: 72.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1Z9S Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.207 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.312 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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