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Open data
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Basic information
Entry | Database: PDB / ID: 1oto | ||||||
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Title | Calcium-binding mutant of the internalin B LRR domain | ||||||
![]() | Internalin B | ||||||
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Function / homology | ![]() peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Marino, M. / Copp, J. / Dramsi, S. / Chapman, T. / van der Geer, P. / Cossart, P. / Ghosh, P. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.9 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1otmC ![]() 1otnC ![]() 1d0bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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![]() ![]() | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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