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Yorodumi- PDB-2nu5: Crystal structure of a complex of griffithsin cocrystallized with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nu5 | ||||||
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Title | Crystal structure of a complex of griffithsin cocrystallized with N-acetylglucosamine | ||||||
Components | griffithsin | ||||||
Keywords | ANTIVIRAL PROTEIN / SUGAR BINDING PROTEIN / griffithsin / lectins / domain swapping / mannose binding / HIV / SARS | ||||||
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 sp. (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.564 Å | ||||||
Authors | Ziolkowska, N.E. / Wlodawer, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine Authors: Ziolkowska, N.E. / Shenoy, S.R. / 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 | 2nu5.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nu5.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nu5 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nu5 | HTTPS FTP |
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-Related structure data
Related structure data | 2nuoC 2gucS 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: 12726.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Griffithsia sp. (eukaryote) / Strain: Q66D336 / Production host: Nicotiana benthamiana (plant) / References: UniProt: P84801 #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to N-acetylglucosamine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Jun 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.564→50 Å / Num. all: 30231 / Num. obs: 30231 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.084 |
Reflection shell | Resolution: 1.564→1.62 Å / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GUC Resolution: 1.564→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.184 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 / 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 mean: 14.397 Å2
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Refinement step | Cycle: LAST / Resolution: 1.564→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.564→1.604 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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