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Yorodumi- PDB-5ajb: X-ray structure of the RSL lectin in complex with Lewis X tetrasa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ajb | |||||||||
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Title | X-ray structure of the RSL lectin in complex with Lewis X tetrasaccahride | |||||||||
Components | LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / LEWIS X / BETA-PROPELLER | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | RALSTONIA SOLANACEARUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Topin, J. / Arnaud, J. / Varrot, A. / Imberty, A. | |||||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: The Hidden Conformation of Lewis X, a Human Histo-Blood Group Antigen, is a Determinant for Recognition by Pathogen Lectins Authors: Topin, J. / Lelimousin, M. / Arnaud, J. / Audfray, A. / Perez, S. / Varrot, A. / Imberty, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ajb.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ajb.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ajb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajb_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5ajb_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 5ajb_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 5ajb_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajb ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajb | HTTPS FTP |
-Related structure data
Related structure data | 5ajcC 2bt9S 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 9733.562 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: D8NA05, UniProt: A0A0S4TLR1*PLUS #2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis X antigen / beta anomer #3: 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)-alpha-D-galactopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | 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: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 27% PEG 6K, 0.1 M TRIS, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97928 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.03 Å / Num. obs: 25606 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BT9 Resolution: 1.8→40.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.282 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / 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: 11.752 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.03 Å
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Refine LS restraints |
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