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Yorodumi- PDB-5gik: Modulation of the affinity of a HIV-1 capsid-directed ankyrin tow... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gik | ||||||
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Title | Modulation of the affinity of a HIV-1 capsid-directed ankyrin towards its viral target through critical amino acid editing | ||||||
Components | Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -S45Y | ||||||
Keywords | PROTEIN BINDING / DARPins / Designed ankyrin repeat | ||||||
Function / homology | Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Chuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. ...Chuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J. | ||||||
Citation | Journal: To Be Published Title: Modulation of the affinity of a HIV-1 capsid-directed ankyrintowards its viral target through critical amino acid editing Authors: Chuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gik.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gik.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gik_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 5gik_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 5gik_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5gik_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5gik ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5gik | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16855.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 1000, reagent alcohol, sodium-phosphate dibasic/citric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.988 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→53.31 Å / Num. obs: 19525 / % possible obs: 75 % / Redundancy: 3.9 % / Net I/σ(I): 28.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→53.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.524 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.625 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→53.31 Å
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Refine LS restraints |
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