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Yorodumi- PDB-2wqw: DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wqw | ||||||
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Title | DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain | ||||||
Components | INTERNALIN B | ||||||
Keywords | CELL INVASION / HGF RECEPTOR LIGAND / LEUCINE-RICH REPEAT / LEUCINE RICH REPEAT / LRR / C-MET LIGAND / VIRULENCE FACTOR | ||||||
Function / homology | Function and homology information peptidoglycan-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: 2.24 Å | ||||||
Authors | Ferraris, D.M. / Heinz, D.W. / Niemann, H.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wqw.cif.gz | 129.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wqw.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wqw_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2wqw_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 2wqw_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2wqw_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqw ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqw | HTTPS FTP |
-Related structure data
Related structure data | 2wquC 2wqvC 2wqxC 1h6tS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | THE BIOLOGICAL UNITS ARE DIMERS FORMED BY DISULFIDE BONDS BETWEEN CYSTEINES 206 AND 227. THE DIMERS ARE 2-FOLD SYMMETRIC AND CONSIST OF TWO CHAINS A OR TWO CHAINS B. |
-Components
#1: Protein | Mass: 32030.586 Da / Num. of mol.: 2 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 36-321 OF LISTERIA MONOCYTOGENES INLB CROSS-LINKED INTO DIMERS BY TWO INTERMOLECULAR DISULFIDE BONDS BETWEEN C206 AND C227 Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) / References: UniProt: P25147, UniProt: P0DQD2*PLUS #2: Chemical | ChemComp-PEG / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLY 206 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 227 TO CYS ...ENGINEERED | |
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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: 2.93 Å3/Da / Density % sol: 57.71 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 9.5 Details: 293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9535 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 37017 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H6T Resolution: 2.24→46.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.37 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.199 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→46.88 Å
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Refine LS restraints |
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