+Open data
-Basic information
Entry | Database: PDB / ID: 4cfi | ||||||
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Title | 3D structure of FliC from Burkholderia pseudomallei | ||||||
Components | FLAGELLIN | ||||||
Keywords | STRUCTURAL PROTEIN / FLAGELLA / EPITOPE / IMMUNE RESPONSE | ||||||
Function / homology | Function and homology information bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region Similarity search - Function | ||||||
Biological species | BURKHOLDERIA PSEUDOMALLEI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Lassaux, P. / Peri, C. / Ferrer-Navarro, M. / Gourlay, L.J. / Conchillo-Sole, O. / Daura, X. / Colombo, G. / Bolognesi, M. | ||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2015 Title: Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia Pseudomallei Flagellin. Authors: Nithichanon, A. / Rinchai, D. / Gori, A. / Lassaux, P. / Peri, C. / Conchillio-Sole, O. / Ferrer-Navarro, M. / Gourlay, L.J. / Nardini, M. / Vila, J. / Daura, X. / Colombo, G. / Bolognesi, M. ...Authors: Nithichanon, A. / Rinchai, D. / Gori, A. / Lassaux, P. / Peri, C. / Conchillio-Sole, O. / Ferrer-Navarro, M. / Gourlay, L.J. / Nardini, M. / Vila, J. / Daura, X. / Colombo, G. / Bolognesi, M. / Lertmemonkolchai, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cfi.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfi.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfi ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfi | HTTPS FTP |
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-Related 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: 25899.211 Da / Num. of mol.: 1 / Fragment: RESIDUES 69-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70944 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.65 % |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 25% PEG 6000 AND 0.1 M LITHIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 |
Detector | Date: Jul 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→24.26 Å / Num. obs: 51380 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3K8V, 1IO1 AND 3V47 Resolution: 1.3→23.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.346 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 12.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→23.83 Å
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Refine LS restraints |
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