+Open data
-Basic information
Entry | Database: PDB / ID: 2xr4 | ||||||
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Title | C-terminal domain of BC2L-C Lectin from Burkholderia cenocepacia | ||||||
Components | LECTIN | ||||||
Keywords | SUGAR BINDING PROTEIN / LUNG / PATHOGEN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA CENOCEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sulak, O. / Cioci, G. / Lameignere, E. / Delia, M. / Wimmerova, M. / Imberty, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Burkholderia Cenocepacia Bc2L-C is a Super Lectin with Dual Specificity and Proinflammatory Activity. Authors: Sulak, O. / Cioci, G. / Lameignere, E. / Balloy, V. / Round, A. / Gutsche, I. / Malinovska, L. / Chignard, M. / Kosma, P. / Aubert, D.F. / Marolda, C.L. / Valvano, M.A. / Wimmerova, M. / Imberty, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xr4.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xr4.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 2xr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xr4_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 2xr4_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 2xr4_validation.xml.gz | 14 KB | Display | |
Data in CIF | 2xr4_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xr4 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xr4 | HTTPS FTP |
-Related structure data
Related structure data | 2bv4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12581.974 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4EH86 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 100 MM SODIUM CITRATE PH 5.5, 2.5 M AMMONIUM SULPHATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 0.93→40 Å / Num. obs: 21834 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2.8 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BV4 Resolution: 1.9→87.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.504 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.501 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→87.37 Å
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Refine LS restraints |
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