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Yorodumi- PDB-2wqu: Internalin domain of Listeria monocytogenes InlB: triclinic cryst... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2wqu | ||||||
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| Title | Internalin domain of Listeria monocytogenes InlB: triclinic crystal form | ||||||
Components | INTERNALIN B | ||||||
Keywords | CELL INVASION / HGF RECEPTOR LIGAND / LEUCINE RICH REPEAT / LRR / C-MET LIGAND / VIRULENCE FACTOR | ||||||
| Function / homology | Function and homology informationpeptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
| Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Niemann, H.H. / Heinz, D.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010Title: Ligand-Mediated Dimerization of the met Receptor Tyrosine Kinase by the Bacterial Invasion Protein Inlb. Authors: Ferraris, D.M. / Gherardi, E. / Di, Y. / Heinz, D.W. / Niemann, H.H. | ||||||
| History |
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| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2wqu.cif.gz | 332.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2wqu.ent.gz | 274.3 KB | Display | PDB format |
| PDBx/mmJSON format | 2wqu.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqu ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqu | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 2wqvC ![]() 2wqwC ![]() 2wqxC ![]() 1h6tS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 6 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
| #1: Protein | Mass: 32243.818 Da / Num. of mol.: 6 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND ...Details: SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS. |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
| Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2006 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
| Reflection | Resolution: 2.6→20 Å / Num. obs: 55139 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 4.96 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.13 |
| Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.59 / % possible all: 74.8 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1H6T Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 25.185 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / 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: 30.64 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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| Refine LS restraints |
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LISTERIA MONOCYTOGENES (bacteria)
X-RAY DIFFRACTION
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