+Open data
-Basic information
Entry | Database: PDB / ID: 7rki | ||||||
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Title | Griffithsin-S10Y/S42Y/S88Y | ||||||
Components | Griffithsin | ||||||
Keywords | SUGAR BINDING PROTEIN / complex | ||||||
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: 2.09 Å | ||||||
Authors | Sun, J.D. / Zhao, G.X. | ||||||
Funding support | United States, 1items
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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 | 7rki.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rki.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rki ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rki | HTTPS FTP |
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-Related structure data
Related structure data | 7riaC 7ribC 7ricC 7ridC 7rkgC 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
#1: Protein | Mass: 15046.390 Da / Num. of mol.: 2 / Mutation: S10Y, S42Y, S88Y 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 #2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.93 Å3/Da / Density % sol: 36.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M citric acid, pH 3.1, 2.6 M sodium chloride |
-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 1, 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: 2.09→25 Å / Num. obs: 13650 / % possible obs: 96.3 % / Redundancy: 7 % / Biso Wilson estimate: 23.22 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1368 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GUC Resolution: 2.09→21.91 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.6737 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: 24.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→21.91 Å
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Refine LS restraints |
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LS refinement shell |
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