+Open data
-Basic information
Entry | Database: PDB / ID: 2axw | ||||||
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Title | Structure of DraD invasin from uropathogenic Escherichia coli | ||||||
Components | DraD invasin | ||||||
Keywords | CELL INVASION / HOMODIMER / BETA-SANDWICH / IMMUNOGLOBULIN-LIKE FOLD / SWAPPED C-TERMINAL STRANDS | ||||||
Function / homology | Function and homology information Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å | ||||||
Authors | Jedrzejczak, R. / Dauter, Z. / Dauter, M. / Piatek, R. / Zalewska, B. / Mroz, M. / Bury, K. / Nowicki, B. / Kur, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structure of DraD invasin from uropathogenic Escherichia coli: a dimer with swapped beta-tails. Authors: Jedrzejczak, R. / Dauter, Z. / Dauter, M. / Piatek, R. / Zalewska, B. / Mroz, M. / Bury, K. / Nowicki, B. / Kur, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axw.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axw.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 2axw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axw ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14713.293 Da / Num. of mol.: 2 / Fragment: DraD invasin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: draD / Plasmid: pInvDsyg-C-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q7BG36, UniProt: Q47038*PLUS #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-GOL / | #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: 1.91 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NaCl, Hepes, glycerol, PEG-2000 MME, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 5, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→30 Å / Num. all: 109502 / Num. obs: 108822 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.05→1.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.9 / Num. unique all: 10677 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.05→29.49 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.311 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.027 / ESU R Free: 0.027 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.984 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20 /
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