+Open data
-Basic information
Entry | Database: PDB / ID: 7rkg | ||||||
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Title | Griffithsin mutant Y28W | ||||||
Components | Griffithsin | ||||||
Keywords | SUGAR BINDING PROTEIN / complex / HIV Inhibitor | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhao, G. / Sun, J. / Bewley, C. | ||||||
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 | 7rkg.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rkg.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 7rkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rkg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7rkg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7rkg_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7rkg_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rkg ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rkg | HTTPS FTP |
-Related structure data
Related structure data | 7riaC 7ribC 7ricC 7ridC 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
#1: Protein | Mass: 14841.136 Da / Num. of mol.: 2 / Mutation: Y28W 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: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 1.5 2.2 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: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 17186 / % possible obs: 97.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.21 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Χ2: 0.342 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 852 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.105 / Rrim(I) all: 0.239 / Χ2: 0.16 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2guc Resolution: 2.2→29.16 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.679 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: 22.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.16 Å
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Refine LS restraints |
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LS refinement shell |
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