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Yorodumi- PDB-3ll2: Monomeric Griffithsin in Complex with a High-Mannose Branched Car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ll2 | |||||||||
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Title | Monomeric Griffithsin in Complex with a High-Mannose Branched Carbohydrate | |||||||||
Components | Griffithsin | |||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / sugar-binding / anti-HIV / high mannose / Man9 / gp120 / gp41 / jacalin-related / Mannose-binding | |||||||||
Function / homology | Function and homology information N-acetylgalactosamine binding / D-glucose binding / D-mannose binding / carbohydrate binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Griffithsia (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | |||||||||
Authors | Moulaei, T. / Wlodawer, A. | |||||||||
Citation | Journal: Structure / Year: 2010 Title: Monomerization of viral entry inhibitor griffithsin elucidates the relationship between multivalent binding to carbohydrates and anti-HIV activity. Authors: Moulaei, T. / Shenoy, S.R. / Giomarelli, B. / Thomas, C. / McMahon, J.B. / Dauter, Z. / O'Keefe, B.R. / Wlodawer, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ll2.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ll2.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ll2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3ll2 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3ll2 | HTTPS FTP |
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-Related structure data
Related structure data | 3lkySC 3ll0C 3ll1C 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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-Components
#1: Protein | Mass: 12818.853 Da / Num. of mol.: 1 / Mutation: Gly-Ser insertion after S16, L2S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Griffithsia (eukaryote) / Strain: Q66D336 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84801 | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M mixture of imidazole, sodium cacodylate, MES, and bis-tris, 0.1 M mixture of L-Na-glutamate, alanine, glycine, lysine-HCl, and serine, 30% w/v PEG MME 550 and PEG 20000, pH 6.5, VAPOR ...Details: 0.1 M mixture of imidazole, sodium cacodylate, MES, and bis-tris, 0.1 M mixture of L-Na-glutamate, alanine, glycine, lysine-HCl, and serine, 30% w/v PEG MME 550 and PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→50 Å / Num. obs: 66935 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.055 / Χ2: 1.185 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2 / Num. unique all: 6566 / Χ2: 0.772 / % possible all: 98.4 |
-Phasing
Phasing MR | Rfactor: 31.44 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LKY Resolution: 0.97→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.983 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.916 / SU B: 0.57 / SU ML: 0.015 / SU R Cruickshank DPI: 0.021 / SU Rfree: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.021 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.74 Å2 / Biso mean: 15.233 Å2 / Biso min: 7.07 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.97→0.995 Å / Total num. of bins used: 20
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