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Open data
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Basic information
Entry | Database: PDB / ID: 2y3c | ||||||
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Title | Treponema denticola variable protein 1 | ||||||
![]() | TREPONEMA DENTICOLA VARIABLE PROTEIN 1 | ||||||
![]() | UNKNOWN FUNCTION / PERIODONTAL DISEASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Le Coq, J. / Ghosh, P. | ||||||
![]() | ![]() Title: Conservation of the C-Type Lectin Fold for Massive Sequence Variation in a Treponema Diversity-Generating Retroelement. Authors: Le Coq, J. / Ghosh, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 446.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 32113.270 Da / Num. of mol.: 1 / Fragment: RESIDUES 39-329 Source method: isolated from a genetically manipulated source Details: DISUFIDE BOND BETWEEN C318 SIDE CHAIN AND BETA-MERCAPTOETHANOL. C318 WAS REPLACED BY A MODIFIED AMINO ACID CME318. Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 100 MM BICINE, PH 7, 2.7-3M SODIUM ACETATE, PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Apr 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.46 Å / Num. obs: 57216 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LIBRARY FOR THE MODIFIED C318 LABELLED CME WAS CREATED IN PRODRG2 AND THERE ARE NUMEROUS AMINO ACIDS WITH ALTERNATE CONFORMATIONS INCLUDING CME318.
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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: 14.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→38.58 Å
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Refine LS restraints |
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