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Yorodumi- PDB-8guv: LecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8guv | |||||||||||||||
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Title | LecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: 134308-13-7) | |||||||||||||||
Components | PA-I galactophilic lectin | |||||||||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / glycomimetics / Pseudomonas aeruginosa | |||||||||||||||
Function / homology | Function and homology information heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | |||||||||||||||
Authors | Kuhaudomlarp, S. / Siebs, E. / Varrot, A. / Imberty, A. / Titz, A. | |||||||||||||||
Funding support | France, Germany, 4items
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Citation | Journal: To Be Published Title: LecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: 134308-13-7) Authors: Siebs, E. / Kuhaudomlarp, S. / Shanina, E. / Varrot, A. / da Silva Fiqueiredo Celestino Gomes, P. / Lerner, C. / Grether, U. / Rademacher, C. / Rognan, D. / Imberty, A. / Titz, A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8guv.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8guv.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 8guv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/8guv ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8guv | HTTPS FTP |
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-Related structure data
Related structure data | 1okoS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121
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-Components
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LecA was produced as a recombinant protein in E. coli without methionine at position 1. Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 24% PEG 2kMME, 0.1 M KSCN, 0.1 M sodium acetate pH 4.5 cocrystallised with tolcapone. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.32→42.84 Å / Num. obs: 56290 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.055 / Net I/σ(I): 25.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OKO Resolution: 1.32→42.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2247 / WRfactor Rwork: 0.2062 / FOM work R set: 0.8594 / SU B: 0.84 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0588 / SU Rfree: 0.0602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 48.8 Å2 / Biso mean: 14.934 Å2 / Biso min: 7.68 Å2
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Refinement step | Cycle: final / Resolution: 1.32→42.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3614 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.321→1.355 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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