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Yorodumi- PDB-1m9s: Crystal structure of Internalin B (InlB), a Listeria monocytogene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m9s | ||||||
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Title | Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains. | ||||||
Components | Internalin B | ||||||
Keywords | SIGNALING PROTEIN / internalin / cell invasion / GW domains / SH3 domains | ||||||
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 / MAD / Resolution: 2.65 Å | ||||||
Authors | Marino, M. / Banerjee, M. / Jonquieres, R. / Cossart, P. / Ghosh, P. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: GW domains of the Listeria monocytogenes invasion protein InlB are SH3-like and mediate binding to host ligands Authors: Marino, M. / Banerjee, M. / Jonquieres, R. / Cossart, P. / Ghosh, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m9s.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m9s.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/1m9s ftp://data.pdbj.org/pub/pdb/validation_reports/m9/1m9s | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Details | The biological assembly is a monomer composed of InlB residues 36 to 630. Residues 320 to 390 are present but disordered. Ambiguity in the position of this disordered region means that the monomer is made up of one N-terminal domain and one C-terminal domain, but there are two possible positions for the C-terminal domain. The alternate position for C-terminal domain is generated by the two fold axis (x = -x, y = y, z = 1/2 - z). |
-Components
#1: Protein | Mass: 68622.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: inlB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25147, UniProt: P0DQD2*PLUS | ||||
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#2: Chemical | ChemComp-TB / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 5.33 Å3/Da / Density % sol: 76.93 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: lithium sulfate, glycerol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.65→50 Å / Num. all: 43356 / Num. obs: 37423 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.65→2.74 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.53 / % possible all: 59 | ||||||||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 59 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.65→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 93.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.274 / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.273 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.65 Å / Lowest resolution: 2.74 Å / Rfactor Rfree: 0.488 / Rfactor Rwork: 0.46 |