+Open data
-Basic information
Entry | Database: PDB / ID: 2r0f | ||||||
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Title | Ligand free structure of fungal lectin CGL3 | ||||||
Components | CGL3 lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / galectin-related / lectin / chitooligosaccharides | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Coprinus cinereus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Waelti, M.A. / Walser, P.J. / Thore, S. / Gruenler, A. / Ban, N. / Kuenzler, M. / Aebi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Basis for Chitotetraose Coordination by CGL3, a Novel Galectin-Related Protein from Coprinopsis cinerea Authors: Waelti, M.A. / Walser, P.J. / Thore, S. / Gruenler, A. / Bednar, M. / Kuenzler, M. / Aebi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0f.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0f.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0f_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 2r0f_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 2r0f_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2r0f_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0f ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0f | HTTPS FTP |
-Related structure data
Related structure data | 2r0hC 1uldS S: Starting model for refinement C: citing same article (ref.) |
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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 domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 1 - 163 / Label seq-ID: 1 - 163
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-Components
#1: Protein | Mass: 18758.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coprinus cinereus (fungus) / Strain: AmutBmut / Gene: cgl3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q206Z5 #2: 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: 4.27 Å3/Da / Density % sol: 71.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: MPD, sodium citrate, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.966 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2005 |
Radiation | Monochromator: Sagittal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 41642 / % possible obs: 91.03 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.828 Å2 / Rsym value: 0.12 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 8 / Num. unique all: 2432 / Rsym value: 0.24 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ULD Resolution: 2→14.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.935 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.135 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2→14.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1312 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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