+Open data
-Basic information
Entry | Database: PDB / ID: 1oto | ||||||
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Title | Calcium-binding mutant of the internalin B LRR domain | ||||||
Components | Internalin B | ||||||
Keywords | CELL ADHESION / internalin / InlB / calcium-binding / invasion / Listeria | ||||||
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: 1.96 Å | ||||||
Authors | Marino, M. / Copp, J. / Dramsi, S. / Chapman, T. / van der Geer, P. / Cossart, P. / Ghosh, P. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Characterization of the calcium-binding sites of Listeria monocytogenes InlB Authors: Marino, M. / Banerjee, M. / Copp, J. / Dramsi, S. / Chapman, T. / Van Der Geer, P. / 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 | 1oto.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oto.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oto_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 1oto_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 1oto_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1oto_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1oto ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1oto | HTTPS FTP |
-Related structure data
Related structure data | 1otmC 1otnC 1d0bS 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: 26172.990 Da / Num. of mol.: 1 / Fragment: LRR domain / Mutation: D59A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Plasmid: pet28b (Novagen) / 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-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 40.77 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Peg 8000, Mes, Calcium acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Marino, M., (1999) Mol.Cell, 4, 1063. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000 / Details: Osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→15 Å / Num. all: 15431 / Num. obs: 15339 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.97 % / Rsym value: 0.053 / Net I/σ(I): 24.23 |
Reflection shell | Resolution: 1.96→2.03 Å / Mean I/σ(I) obs: 3.18 / Rsym value: 0.493 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 15 Å / % possible obs: 99 % / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1d0b Resolution: 1.96→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.96→15 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.189 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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