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Yorodumi- PDB-5a6z: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a6z | |||||||||
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Title | Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis a | |||||||||
Components | LECB | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / LECB / LEWIS ANTIGEN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Sommer, R. / Wagner, S. / Varrot, A. / Khaledi, A. / Haussler, S. / Imberty, A. / Titz, A. | |||||||||
Citation | Journal: Chem Sci / Year: 2016 Title: The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery. Authors: Sommer, R. / Wagner, S. / Varrot, A. / Nycholat, C.M. / Khaledi, A. / Haussler, S. / Paulson, J.C. / Imberty, A. / Titz, 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 | 5a6z.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a6z.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a6z_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5a6z_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5a6z_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 5a6z_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a6z ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a6z | HTTPS FTP |
-Related structure data
Related structure data | 5a6qSC 5a6xC 5a6yC 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
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 875 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | TERMINAL 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: 2.34 Å3/Da / Density % sol: 47.48 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 22% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5. PEG CONCENTRATION WAS INCREASED TO 30% FOR CRYOPROTECTION |
-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: 1.5→27.82 Å / Num. obs: 66333 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.6 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A6Q Resolution: 1.5→27.82 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.973 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. LOCAL NCS
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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: 11.339 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.82 Å
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Refine LS restraints |
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