+Open data
-Basic information
Entry | Database: PDB / ID: 5jny | ||||||
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Title | Crystal Structure of 10E8 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MPER / HIV / antibody / neutralizing | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ISOPROPYL ALCOHOL Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.041 Å | ||||||
Authors | Ofek, G. / Kwong, P. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. Authors: Soto, C. / Ofek, G. / Joyce, M.G. / Zhang, B. / McKee, K. / Longo, N.S. / Yang, Y. / Huang, J. / Parks, R. / Eudailey, J. / Lloyd, K.E. / Alam, S.M. / Haynes, B.F. / Mullikin, J.C. / ...Authors: Soto, C. / Ofek, G. / Joyce, M.G. / Zhang, B. / McKee, K. / Longo, N.S. / Yang, Y. / Huang, J. / Parks, R. / Eudailey, J. / Lloyd, K.E. / Alam, S.M. / Haynes, B.F. / Mullikin, J.C. / Connors, M. / Mascola, J.R. / Shapiro, L. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jny.cif.gz | 340.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jny.ent.gz | 288.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jny ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jny | HTTPS FTP |
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-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: 25318.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 22902.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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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: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6% PEG 8000, 25% Isopropanol, 0.1 M Imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.05→50 Å / Num. obs: 37419 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.07 / Rrim(I) all: 0.232 / Χ2: 0.964 / Net I/av σ(I): 10.4 / Net I/σ(I): 3.5 / Num. measured all: 397174 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.041→32.836 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.041→32.836 Å
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Refine LS restraints |
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LS refinement shell |
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