+Open data
-Basic information
Entry | Database: PDB / ID: 4csd | ||||||
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Title | Structure of Monomeric Ralstonia solanacearum lectin | ||||||
Components | FUCOSE-BINDING LECTIN PROTEIN | ||||||
Keywords | FUCOSE-BINDING PROTEIN / BETA PROPELLER | ||||||
Function / homology | Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta / methyl alpha-L-fucopyranoside / Fucose-binding lectin protein Function and homology information | ||||||
Biological species | RALSTONIA SOLANACEARUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Arnaud, J. / Trundle, K. / Claudinon, J. / Audfray, A. / Varrot, A. / Romer, W. / Imberty, A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Membrane Deformation by Neolectins with Engineered Glycolipid Binding Sites. Authors: Arnaud, J. / Trondle, K. / Claudinon, J. / Audfray, A. / Varrot, A. / Romer, W. / Imberty, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4csd.cif.gz | 245.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4csd.ent.gz | 198.6 KB | Display | PDB format |
PDBx/mmJSON format | 4csd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4csd ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4csd | HTTPS FTP |
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-Related structure data
Related structure data | 2bt9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 1 - 270 / Label seq-ID: 2 - 271
NCS oper: (Code: given Matrix: (-0.9999, 0.001556, -0.01016), Vector: |
-Components
#1: Protein | Mass: 29349.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MONOMERIC CHIMERA OF THE WILD TYPE RSL / Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Plasmid: PET-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q8XXK6 #2: Sugar | ChemComp-MFU / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | AMINO ACIDS 0 TO 88 OF MONOMERIC RSL CORRESPOND TO AMINO ACIDS 1 TO 89 OF RSL. AMINO ACIDS 95 TO ...AMINO ACIDS 0 TO 88 OF MONOMERIC RSL CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.22 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M TRIS HYDROCHLORIDE PH 8.5, 2M AMMONIUM SULFATE |
-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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→41.92 Å / Num. obs: 99018 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.6 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BT9 Resolution: 1.35→41.92 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.324 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→41.92 Å
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Refine LS restraints |
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