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Yorodumi- PDB-2wv6: Crystal structure of the cholera toxin-like B-subunit from Citrob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wv6 | ||||||
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Title | Crystal structure of the cholera toxin-like B-subunit from Citrobacter freundii to 1.9 angstrom | ||||||
Components | CFXB | ||||||
Keywords | TOXIN / LECTIN / B SUBUNIT / CHOLERA TOXIN-LIKE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CITROBACTER FREUNDII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å | ||||||
Authors | Jansson, L. / Lebens, M. / Imberty, A. / Varrot, A. / Teneberg, S. | ||||||
Citation | Journal: Biochimie / Year: 2010 Title: Carbohydrate Binding Specificities and Crystal Structure of the Cholera Toxin-Like B-Subunit from Citrobacter Freundii. Authors: Jansson, L. / Angstrom, J. / Lebens, M. / Imberty, A. / Varrot, A. / Teneberg, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wv6.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wv6.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wv6_validation.pdf.gz | 521.2 KB | Display | wwPDB validaton report |
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Full document | 2wv6_full_validation.pdf.gz | 535.8 KB | Display | |
Data in XML | 2wv6_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 2wv6_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wv6 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wv6 | HTTPS FTP |
-Related structure data
Related structure data | 3efxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11696.230 Da / Num. of mol.: 10 / Fragment: B SUBUNIT, RESIDUES 23-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Plasmid: PML-HCFXBTAC / Production host: VIBRIO CHOLERAE (bacteria) / Strain (production host): JS1569 / References: UniProt: Q8GAV5 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE FIRST 22 AMINO ACID CORRESPOND TO THE PEPTIDE SIGNAL. OUR NUMBERING START AT THE FIRST RESIDUE ...THE FIRST 22 AMINO ACID CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 10% PEG 6K, 1 M LITHIUM CHLORIDE AND 100 MM SODIUM ACETATE PH 4.6. 20% GLYECROL WERE ADDED AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.895→43.9 Å / Num. obs: 71465 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EFX Resolution: 1.895→40.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.003 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.141 / 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: 16.686 Å2
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Refinement step | Cycle: LAST / Resolution: 1.895→40.9 Å
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Refine LS restraints |
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