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Yorodumi- PDB-5a70: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a70 | |||||||||
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Title | Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide | |||||||||
Components | LECB | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / LECB LEWIS X ANTIGEN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Sommer, R. / Wagner, S. / Varrot, A. / Khaledi, A. / Haussler, S. / Imberty, A. / Titz, A. | |||||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Authors: Lepsik, M. / Sommer, R. / Kuhaudomlarp, S. / Lelimousin, M. / Paci, E. / Varrot, A. / Titz, A. / Imberty, A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a70.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a70.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 5a70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a70 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a70 | HTTPS FTP |
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-Related structure data
Related structure data | 6r35C 5a6qS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11676.710 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: UCBPP-PA14 / Plasmid: PRS01.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U8MRX2, UniProt: A0A0H2ZE85*PLUS #2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | NTERMINAL METHIONINE | |
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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: 2.29 Å3/Da / Density % sol: 46.43 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 30% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98021 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98021 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→44.94 Å / Num. obs: 53856 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 74.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A6Q Resolution: 1.6→44.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.573 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / 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 mean: 14.432 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→44.94 Å
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Refine LS restraints |
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