+Open data
-Basic information
Entry | Database: PDB / ID: 3ohn | ||||||
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Title | Crystal structure of the FimD translocation domain | ||||||
Components | Outer membrane usher protein FimD | ||||||
Keywords | MEMBRANE PROTEIN / beta-barrel / protein translocation / outer membrane | ||||||
Function / homology | Function and homology information fimbrial usher porin activity / pilus assembly / cell outer membrane / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.011 Å | ||||||
Authors | Wang, T. / Li, H. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate. Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. ...Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. / Hultgren, S.J. / Thanassi, D.G. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ohn.cif.gz | 191.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ohn.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ohn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ohn_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 3ohn_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 3ohn_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3ohn_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/3ohn ftp://data.pdbj.org/pub/pdb/validation_reports/oh/3ohn | HTTPS FTP |
-Related structure data
Related structure data | 3rfzC 2vqiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 61537.316 Da / Num. of mol.: 2 / Fragment: TRANSLOCATION DOMAIN (unp residues 169-708) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Plasmid: pNH297 / Production host: Escherichia coli (E. coli) / Strain (production host): B tuner / References: UniProt: C8U0R5, UniProt: P30130*PLUS |
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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: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM Trisodium citrate,pH4.8~6.5, 7% (w/v) PEG4000, 100mM sodium chloride, 50mM Magnesium, 20mM spermine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 27375 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.115 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.5 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2vqi Resolution: 3.011→28.89 Å / SU ML: 0.44 / σ(F): 1.97 / Phase error: 33.22 / Stereochemistry target values: ML Details: AUTHORS HAVE APPROVED THIS ENTRY WITH REPORTED R VALUE AS 0.23 WHILE CALCULATED R VALUE IS 0.31. THE DEPOSITED COORDINATES WERE FURTHER MODIFIED IN COOT AFTER FINAL ROUND OF PHENIX REFINEMENT.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.835 Å2 / ksol: 0.29 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.8 Å2
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Refinement step | Cycle: LAST / Resolution: 3.011→28.89 Å
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Refine LS restraints |
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LS refinement shell |
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