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Yorodumi- PDB-5fsb: Structure of tectonin 2 from laccaria bicolor in complex with 2-o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fsb | ||||||
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Title | Structure of tectonin 2 from laccaria bicolor in complex with 2-o-methyl-methyl-seleno-beta-l-fucopyranoside | ||||||
Components | TECTONIN 2 | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / METHYLATED SUGAR / NEMATOXIC / BETA-PROPELLER | ||||||
Function / homology | Tectonin domain / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / methyl 1-seleno-2-O-methyl-beta-L-fucopyranoside / BORIC ACID / Tectonin 2 Function and homology information | ||||||
Biological species | LACCARIA BICOLOR (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Sommer, R. / Bleuer, S. / Titz, A. / Kunzler, M. / Varrot, A. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Crystal Structures of Fungal Tectonin in Complex with O-Methylated Glycans Suggest Key Role in Innate Immune Defense. Authors: Sommer, R. / Makshakova, O.N. / Wohlschlager, T. / Hutin, S. / Marsh, M. / Titz, A. / Kunzler, M. / Varrot, 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 | 5fsb.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fsb.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fsb_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 5fsb_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 5fsb_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 5fsb_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fsb ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fsb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.982, -0.141, 0.124), Vector: |
-Components
-Protein / Sugars , 2 types, 13 molecules AB
#1: Protein | Mass: 23813.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACCARIA BICOLOR (fungus) / Strain: S238N-H82 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0CZL6 #3: Sugar | ChemComp-6YR / |
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-Non-polymers , 4 types, 526 molecules
#2: Chemical | #4: Chemical | #5: Chemical | ChemComp-BO3 / | #6: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.71 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 1.6M MAGNESIUM SULFATE 0.1M MES PH 6.5. 80% LITHIUM SULFATE WAS USED AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97914 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34.53 Å / Num. obs: 39383 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.65→34.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.716 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. B MOLECULES HAVE THREE STATISTICAL ORIENTATIONS IN THE CRYSTAL AND TO PRODUCE THEM IT WAS CONSTRUCTED AROUND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. B MOLECULES HAVE THREE STATISTICAL ORIENTATIONS IN THE CRYSTAL AND TO PRODUCE THEM IT WAS CONSTRUCTED AROUND TEH THREE FOLD AXIS WITH 0.33 OCCUPANCY DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. MOLECULE B WAS BUILD WITH 0.33 OCCUPANCY TO CREATE BY SYMMETRY THE THREE ORIENTATIONS FOUND IN THE CRYSTAL
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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: 9.051 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.53 Å
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Refine LS restraints |
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