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Yorodumi- PDB-4cp9: Crystal structure OF lecA lectin complexed with a divalent galact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cp9 | ||||||
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Title | Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom | ||||||
Components | (PA-I GALACTOPHILIC ...) x 2 | ||||||
Keywords | SUGAR BINDING PROTEIN / GALACTOSE BINDING / SUGAR BASED INHIBITOR | ||||||
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: 1.65 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D | ||||||
Authors | Topin, J. / Varrot, A. / Imberty, A. / Wissinger, N. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa. Authors: Novoa, A. / Eierhoff, T. / Topin, J. / Varrot, A. / Barluenga, S. / Imberty, A. / Romer, W. / Winssinger, N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cp9.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cp9.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cp9 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cp9 | HTTPS FTP |
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-Related structure data
Related structure data | 4cpbC 1okoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-PA-I GALACTOPHILIC ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 12834.134 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: OXIDATED CYS57 / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097 |
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#2: Protein | Mass: 12818.134 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: OXIDATED CYS57 / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097 |
-Sugars , 1 types, 4 molecules
#4: Sugar | ChemComp-GAL / |
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-Non-polymers , 6 types, 434 molecules
#3: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CN8 / ( #6: Chemical | ChemComp-1PE / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | 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: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: SOLUTION 20 OF THE CSSI SCREEN 8% PEG 20K, 8% PEG550MME, 100 MM TRIS 8.5 AND 0.2 M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESERACH / Detector: CCD / Date: Jul 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→48.47 Å / Num. obs: 65807 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OKO Resolution: 1.65→48.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.38 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS 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: 26.643 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→48.47 Å
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Refine LS restraints |
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