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Yorodumi- PDB-7pv8: InlB392_T332E: T332E variant of Listeria monocytogenes InlB (inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pv8 | ||||||
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Title | InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392 | ||||||
Components | Internalin B | ||||||
Keywords | CELL INVASION / LEUCINE RICH REPEAT / PROTEIN BINDING / PATHOGENICITY / 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 / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Geerds, C. / Niemann, H.H. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat. Authors: Geerds, C. / Bleymuller, W.M. / Meyer, T. / Widmann, C. / Niemann, H.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pv8.cif.gz | 271.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pv8.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 7pv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pv8 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pv8 | HTTPS FTP |
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-Related structure data
Related structure data | 7nmsC 7pv9C 1h6tS 2y5pS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40449.801 Da / Num. of mol.: 1 / Mutation: T332E Source method: isolated from a genetically manipulated source Details: residue 36 to 392 of InlB with five N-terminal residues (GPLGS) remaining after human rhinovirus C3 protease (PreScission) cleavage of the GST-tag Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: inlB, lmo0434 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P0DQD2 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition G2): 0.1 M (imidazole / MES), pH 6.5; 20 % v/v ethylene glycol; 10 % w/v PEG 8,000; 0.02 M sodium formate; 0.02 M ...Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition G2): 0.1 M (imidazole / MES), pH 6.5; 20 % v/v ethylene glycol; 10 % w/v PEG 8,000; 0.02 M sodium formate; 0.02 M ammonium acetate; 0.02 M sodium citrate tribasic dehydrate; 0.02 M sodium potassium tartrate tetrahydrate; 0.02 M sodium oxamate; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jan 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 35861 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.122 / Net I/σ(I): 16.56 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2598 / CC1/2: 0.792 / Rrim(I) all: 1.956 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H6T, 2Y5P Resolution: 2.05→16.15 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1443 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→16.15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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