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Yorodumi- PDB-4or1: Structure and mechanism of fibronectin binding and biofilm format... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4or1 | ||||||
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Title | Structure and mechanism of fibronectin binding and biofilm formation of enteroaggregative Escherischia coli AAF fimbriae | ||||||
Components | Invasin homolog AafB, Major fimbrial subunit of aggregative adherence fimbria II AafA chimeric construct | ||||||
Keywords | CELL ADHESION / biofilm / chaperone-usher / pilus / adhesion / fibronectin / fimbriae / fibre / immunoglobulin-like / Outer membrane pilus | ||||||
Function / homology | Function and homology information Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lee, W.-C. / Garnett, J.A. / Yang, Y. / Matthews, S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Structural insight into host recognition by aggregative adherence fimbriae of enteroaggregative Escherichia coli. Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J. ...Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J.P. / Zavialov, A.V. / Matthews, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4or1.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4or1.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 4or1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4or1_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 4or1_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 4or1_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4or1_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4or1 ftp://data.pdbj.org/pub/pdb/validation_reports/or/4or1 | HTTPS FTP |
-Related structure data
Related structure data | 2mpvC 4ph8C 4phxC 2axwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17186.150 Da / Num. of mol.: 2 Fragment: AAF/II pilus minor pilin, unp residues 24-146 and unp residues 25-34 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Enteroaggregative 042 / Gene: aafB, aafA / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q9X4L4, UniProt: O30595 #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-ACT / | #4: 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: 3.13 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M BIS-TRIS, 0.2 M LiSO4, 25% PEG3350., pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3→51.24 Å / Num. all: 9081 / Num. obs: 9081 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 74.4 Å2 / Rsym value: 0.111 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1302 / Rsym value: 0.374 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AXW Resolution: 3→51.24 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.549 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.995 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 56.38 Å2
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Refinement step | Cycle: LAST / Resolution: 3→51.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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