+Open data
-Basic information
Entry | Database: PDB / ID: 7rid | ||||||
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Title | Griffithsin variant Y28A | ||||||
Components | Griffithsin | ||||||
Keywords | SUGAR BINDING PROTEIN / complex / mannose binding protein | ||||||
Function / homology | Function and homology information N-acetylgalactosamine binding / glucose binding / mannose binding / carbohydrate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Griffithsia sp. (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhao, G. / Sun, J. / Bewley, C.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: C 3 -Symmetric Aromatic Core of Griffithsin Is Essential for Potent Anti-HIV Activity. Authors: Sun, J. / Zhao, G. / Bylund, T. / Lee, M. / Adibhatla, S. / Kwong, P.D. / Chuang, G.Y. / Rawi, R. / Bewley, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rid.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rid.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 7rid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/7rid ftp://data.pdbj.org/pub/pdb/validation_reports/ri/7rid | HTTPS FTP |
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-Related structure data
Related structure data | 7riaC 7ribC 7ricC 7rkgC 7rkiC 2gucS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14726.003 Da / Num. of mol.: 1 / Mutation: Y28A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Griffithsia sp. (strain Q66D336) (eukaryote) Strain: Q66D336 / Production host: Escherichia coli (E. coli) / References: UniProt: P84801 |
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#2: 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: 3.68 Å3/Da / Density % sol: 66.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M bis-tris, pH 6.5 0.2 M calcium chloride dihydrate 45% v/v (+/-)-2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 10413 / % possible obs: 99.9 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 511 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GUC Resolution: 2.3→25.31 Å / Cross valid method: FREE R-VALUE / σ(F): 100 / Phase error: 12.3684 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.34 Å
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