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Yorodumi- PDB-2wqx: InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Liste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wqx | ||||||
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Title | InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant 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 / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Niemann, H.H. / Ferraris, D.M. / Heinz, D.W. | ||||||
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 | 2wqx.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wqx.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wqx_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 2wqx_full_validation.pdf.gz | 430.7 KB | Display | |
Data in XML | 2wqx_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 2wqx_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqx ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqx | HTTPS FTP |
-Related structure data
Related structure data | 2wquC 2wqvC 2wqwC 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:
NCS oper: (Code: given Matrix: (0.99991, -0.01073, 0.00801), Vector: |
-Components
#1: Protein | Mass: 32510.229 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 4R MUTANT Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P25147, UniProt: P0DQD2*PLUS #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 199 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASP 200 TO ARG ...ENGINEERED | Sequence details | RESIDUES 33-35 REMAIN AFTER TEV CLEAVAGE OF THE GST-FUSION PROTEIN | |
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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: 2.14 Å3/Da / Density % sol: 0.42 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 |
Detector | Type: RIGAKU SATURN 944PLUS / Detector: CCD / Date: Apr 8, 2009 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→20 Å / Num. obs: 33525 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 20.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.65 |
Reflection shell | Resolution: 2.03→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.02 / % possible all: 68.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H6T Resolution: 2.03→38.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.832 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: 12.299 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→38.63 Å
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Refine LS restraints |
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