+Open data
-Basic information
Entry | Database: PDB / ID: 5u65 | ||||||
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Title | Camel Nanobody VHH-5 | ||||||
Components | VHH-5 | ||||||
Keywords | IMMUNE SYSTEM / neutralizing antibody / HIV-1 / nanobody VHH | ||||||
Biological species | Camelus dromedarius (Arabian camel) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Stanfield, R.L. / Wilson, I.A. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers. Authors: Koch, K. / Kalusche, S. / Torres, J.L. / Stanfield, R.L. / Danquah, W. / Khazanehdari, K. / von Briesen, H. / Geertsma, E.R. / Wilson, I.A. / Wernery, U. / Koch-Nolte, F. / Ward, A.B. / Dietrich, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u65.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u65.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 5u65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u65_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 5u65_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 5u65_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 5u65_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u65 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u65 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 14800.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | 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: 2.07 Å3/Da / Density % sol: 39.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.9M ammonium sulfate, 0.1M bicine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→55.3 Å / Num. obs: 10575 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.927 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→55.3 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.684 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.269 / 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: 22.892 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→55.3 Å
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Refine LS restraints |
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