+Open data
-Basic information
Entry | Database: PDB / ID: 2y3c | ||||||
---|---|---|---|---|---|---|---|
Title | Treponema denticola variable protein 1 | ||||||
Components | TREPONEMA DENTICOLA VARIABLE PROTEIN 1 | ||||||
Keywords | UNKNOWN FUNCTION / PERIODONTAL DISEASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TREPONEMA DENTICOLA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Le Coq, J. / Ghosh, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y3c.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y3c.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 2y3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/2y3c ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3c | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) TREPONEMA DENTICOLA (bacteria) / Strain: 35405 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73KE9 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: NONE |
---|---|
Crystal grow | pH: 7 / Details: 100 MM BICINE, PH 7, 2.7-3M SODIUM ACETATE, PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.58 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.547 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→38.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|