[English] 日本語
Yorodumi- PDB-8h63: Crystal structure of Internalin A from Listeria monocytogenes wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h63 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound | ||||||
Components |
| ||||||
Keywords | CELL INVASION/IMMUNE SYSTEM / Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / extracellular region Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Caaveiro, J.M.M. / Nagatoish, S. / Tsumoto, K. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. Authors: Yamazaki, T. / Nagatoishi, S. / Yamawaki, T. / Nozawa, T. / Matsunaga, R. / Nakakido, M. / Caaveiro, J.M.M. / Nakagawa, I. / Tsumoto, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8h63.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8h63.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/8h63 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/8h63 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8h62SC 8h64C 6jb9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 49914.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: inlA, lmo0433,intlA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DJM0 |
---|---|
#2: Antibody | Mass: 12732.190 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria) |
-Non-polymers , 5 types, 770 molecules
#3: Chemical | ChemComp-EPE / | ||||
---|---|---|---|---|---|
#4: Chemical | ChemComp-IPA / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.085 M HEPES sodium pH 7.0; 8.5% Isopropanol; 20% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→33.3 Å / Num. obs: 91994 / % possible obs: 96.6 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12582 / CC1/2: 0.752 / Rpim(I) all: 0.294 / % possible all: 91 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8H62 6JB9 Resolution: 1.53→31.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.412 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.15 Å2 / Biso mean: 15.245 Å2 / Biso min: 6.68 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→31.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|