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Yorodumi- PDB-2gue: Crystal structure of a complex of griffithsin with N-acetylglucosamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gue | ||||||
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Title | Crystal structure of a complex of griffithsin with N-acetylglucosamine | ||||||
Components | griffithsin | ||||||
Keywords | SUGAR BINDING PROTEIN / griffithsin / lectins / domain swapping / mannose binding / HIV / SARS | ||||||
Function / homology | Function and homology information N-acetylgalactosamine binding / glucose binding / mannose binding / carbohydrate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Griffithsia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Ziolkowska, N.E. / Wlodawer, A. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding. Authors: Ziolkowska, N.E. / O'keefe, B.R. / Mori, T. / Zhu, C. / Giomarelli, B. / Vojdani, F. / Palmer, K.E. / McMahon, J.B. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gue.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gue.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/2gue ftp://data.pdbj.org/pub/pdb/validation_reports/gu/2gue | HTTPS FTP |
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-Related structure data
Related structure data | 2gtySC 2gucC 2gudC 2guxC 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 (eukaryote) / Genus: Griffithsia / Production host: Nicotiana benthamiana (plant) / References: UniProt: P84801 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Sugar | ChemComp-NAG / | #5: 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: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.2 M ammonium sulfate, 30% PEG 4000; crystal soaked in a reservoir solution supplemented with 50mM N-acetylglucosamine, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. all: 13606 / Num. obs: 13606 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Rsym value: 0.085 |
Reflection shell | Resolution: 2.02→2.09 Å / % possible all: 56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GTY Resolution: 2.02→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.632 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.23 / 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: 29.875 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.076 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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