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Yorodumi- PDB-5afo: Long Polar Fimbriae adhesin LpfD from the adherent invasive E. co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5afo | ||||||
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Title | Long Polar Fimbriae adhesin LpfD from the adherent invasive E. coli strain LF82 | ||||||
Components | FIMBRIAE | ||||||
Keywords | CELL ADHESION / LONG POLAR FIMBRIAE / AIEC / CROHN'S DISEASE / ADHESIN / PILI | ||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / Fimbriae / : Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.82 Å | ||||||
Authors | Coppens, F. / Iyyathurai, J. / Remaut, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural and Adhesive Properties of the Long Polar Fimbriae Protein Lpfd from Adherent-Invasive Escherichia Coli. Authors: Coppens, F. / Iyyathurai, J. / Ruer, S. / Fioravanti, A. / Taganna, J. / Vereecke, L. / De Greve, H. / Remaut, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5afo.cif.gz | 284.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5afo.ent.gz | 245.8 KB | Display | PDB format |
PDBx/mmJSON format | 5afo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5afo ftp://data.pdbj.org/pub/pdb/validation_reports/af/5afo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.975, 0.003, 0.22), Vector: |
-Components
#1: Protein | Mass: 38626.824 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-350 Source method: isolated from a genetically manipulated source Details: LPFD SELF-COMPLEMENTED BY C-TERMINAL ADDITION OF THE N-TERMINAL EXTENSION OF THE MINOR PILUS SUBUNIT LPFE ATTDLGAKGTLKFSLKISQG Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: LF82 / Description: PROVIDED BY A. DARFEUILLE-MICHAUD / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: E2QGQ5, UniProt: A0A0M3KL51*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | REMOVED FIRST 24 RESIDUES CORRESPONDING TO SIGNAL PEPTIDE, ADDED RESIDUES ...REMOVED FIRST 24 RESIDUES CORRESPOND | |
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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: 56 % Description: PHASES OBTAINED BY SAD EXPERIMENT ON TYROSINE- IODINATED CRYSTAL |
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Crystal grow | pH: 8 Details: 0.1 M TRIS PH 8.0, 0.18 M SODIUM CITRATE, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→49 Å / Num. obs: 82152 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.95 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.63 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.82→48.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.251 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / 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: 30.964 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→48.59 Å
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Refine LS restraints |
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