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Yorodumi- PDB-5lo7: Crystal structure of self-complemented MyfA, the major subunit of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lo7 | |||||||||
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Title | Crystal structure of self-complemented MyfA, the major subunit of Myf fimbriae from Yersinia enterocolitica | |||||||||
Components | Fimbrial protein MyfA,Fimbrial protein MyfA | |||||||||
Keywords | CELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation | |||||||||
Function / homology | Immunoglobulin-like - #3590 / : / Ph 6 antigen / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / Fimbrial protein MyfA Function and homology information | |||||||||
Biological species | Yersinia enterocolitica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | |||||||||
Authors | Pakharukova, N.A. / Roy, S. / Tuitilla, M. / Zavialov, A.V. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: Mol.Microbiol. / Year: 2016 Title: Structural basis for Myf and Psa fimbriae-mediated tropism of pathogenic strains of Yersinia for host tissues. Authors: Pakharukova, N. / Roy, S. / Tuittila, M. / Rahman, M.M. / Paavilainen, S. / Ingars, A.K. / Skaldin, M. / Lamminmaki, U. / Hard, T. / Teneberg, S. / 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 | 5lo7.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lo7.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5lo7 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5lo7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ln4C 5ln8C 5lndSC 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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Unit cell |
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-Components
#1: Protein | Mass: 14555.698 Da / Num. of mol.: 2 / Fragment: UNP residues 51-159,UNP residues 30-47 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: myfA / Plasmid: pET101D / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P33406 #2: Chemical | ChemComp-PG0 / | #3: 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: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 35% dioxane v/v |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: k,h,-l / Fraction: 0.29 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→150.83 Å / Num. all: 25547 / Num. obs: 25547 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.099 / Rsym value: 0.085 / Net I/av σ(I): 6.869 / Net I/σ(I): 9.6 / Num. measured all: 94487 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LND Resolution: 1.9→29.681 Å / FOM work R set: 0.8083 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.15 Å2 / Biso mean: 26.61 Å2 / Biso min: 10.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→29.681 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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