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Yorodumi- PDB-3zdv: Crystal structure of the LecB lectin from Pseudomonas aeruginosa ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zdv | ||||||
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Title | Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside | ||||||
Components | FUCOSE-BINDING LECTIN PA-IIL | ||||||
Keywords | SUGAR BINDING PROTEIN / GLYCOMIMETIC / INHIBITOR | ||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Hauck, D. / Joachim, I. / Frommeyer, B. / Varrot, A. / Philipp, B. / MOller, H.M. / Imberty, A. / Exner, T.E. / Titz, A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes. Authors: Hauck, D. / Joachim, I. / Frommeyer, B. / Varrot, A. / Philipp, B. / Moller, H.M. / Imberty, A. / Exner, T.E. / 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 | 3zdv.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zdv.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zdv_validation.pdf.gz | 501.1 KB | Display | wwPDB validaton report |
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Full document | 3zdv_full_validation.pdf.gz | 507.3 KB | Display | |
Data in XML | 3zdv_validation.xml.gz | 25 KB | Display | |
Data in CIF | 3zdv_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdv ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdv | HTTPS FTP |
-Related structure data
Related structure data | 3dcqS S: Starting model for refinement |
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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 / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 11865.905 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5 #3: Sugar | ChemComp-MMA / |
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-Non-polymers , 6 types, 468 molecules
#2: Chemical | ChemComp-CA / #4: Chemical | ChemComp-F1A / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE N-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: 1.89 Å3/Da / Density % sol: 34.93 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 330 MM SODIUM CACODYLATE PH 6.5 200 MM AMMONIUM SULPHATE 30% PEG8K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→42.25 Å / Num. obs: 76102 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.41→1.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DCQ Resolution: 1.41→42.24 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.632 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED SIDE CHAIN WERE MODELED STEREOCHEMICALLY
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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: 13.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→42.24 Å
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Refine LS restraints |
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