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Yorodumi- PDB-5dfk: Crystal Structure of the Escherichia coli Common Pilus Chaperone, EcpB -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dfk | ||||||
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Title | Crystal Structure of the Escherichia coli Common Pilus Chaperone, EcpB | ||||||
Components | Probable fimbrial chaperone EcpB | ||||||
Keywords | STRUCTURAL PROTEIN / chaperone usher / pilus / pili / biofilm / adhesion / biogenesis / E. coli / virulence | ||||||
Function / homology | EcpB, C-terminal / EcpB C-terminal domain / PapD-like superfamily / Immunoglobulin-like fold / Probable fimbrial chaperone EcpB / Probable fimbrial chaperone EcpB Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å | ||||||
Authors | Garnett, J.A. / Diallo, M. / Matthews, S.J. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis. Authors: Pakharukova, N. / Garnett, J.A. / Tuittila, M. / Paavilainen, S. / Diallo, M. / Xu, Y. / Matthews, S.J. / Zavialov, A.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dfk.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dfk.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dfk_validation.pdf.gz | 420.9 KB | Display | wwPDB validaton report |
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Full document | 5dfk_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 5dfk_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5dfk_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5dfk ftp://data.pdbj.org/pub/pdb/validation_reports/df/5dfk | HTTPS FTP |
-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: 24261.309 Da / Num. of mol.: 1 / Fragment: UNP residues 21-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecpB, matC, ECS88_0289 / Production host: Escherichia coli CFT073 (bacteria) / References: UniProt: B7MCA3, UniProt: P77188*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% (v/v) glycerol, 15% (w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→54.26 Å / Num. obs: 11265 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 32.306 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 44.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 6.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.4→54.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.018 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.217 / 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: 42.69 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→54.26 Å
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Refine LS restraints |
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