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Yorodumi- PDB-5bzw: Crystal Structure of PCDN-27B, an antibody from the PCDN family o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bzw | ||||||
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Title | Crystal Structure of PCDN-27B, an antibody from the PCDN family of HIV-1 antibodies | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV / Antibody / Fab | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Garces, F. / WILSON, I.A. | ||||||
Citation | Journal: Immunity / Year: 2016 Title: Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch. Authors: MacLeod, D.T. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.H. / Ramos, A. / Bian, C.B. / Wickramasinghe, L. / Kong, L. / ...Authors: MacLeod, D.T. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.H. / Ramos, A. / Bian, C.B. / Wickramasinghe, L. / Kong, L. / Eren, K. / Wu, C.Y. / Wong, C.H. / Kosakovsky Pond, S.L. / Wilson, I.A. / Burton, D.R. / Poignard, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bzw.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bzw.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/5bzw ftp://data.pdbj.org/pub/pdb/validation_reports/bz/5bzw | HTTPS FTP |
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-Related structure data
Related structure data | 1rrhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 23306.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EIVLTQSPGTLSLSPGERATLSCRASQSVSAKNLAWYQQKPGQTPRLLMYGVSLRNTGVP ...Details: EIVLTQSPGTLSLSPGERATLSCRASQSVSAKNLAWYQQKPGQTPRLLMYGVSLRNTGVP DRFSGSGSGTDFTLTISRLEPEDSAVYFCQQYGTSPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||
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#2: Antibody | Mass: 25121.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: QVQLQQWGAGLLKPSETLSLTCAVYNESLSAFSWSWIRQFPGQGLEWIGEIDHTTSSNYN PSLKRRINISIDTSKKQFSLKLYSVTAADTAVYYCARGGRKVYHAYWSGYVNNCFDPWGQ ...Details: QVQLQQWGAGLLKPSETLSLTCAVYNESLSAFSWSWIRQFPGQGLEWIGEIDHTTSSNYN PSLKRRINISIDTSKKQFSLKLYSVTAADTAVYYCARGGRKVYHAYWSGYVNNCFDPWGQ GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||
#3: Chemical | ChemComp-SO4 / #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.08 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 3350, 10% (v/v) ethylene glycol and 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 273.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.629 Å / Num. obs: 11743 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rsym value: 0.28 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRH Resolution: 2.9→43.629 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.17 / 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: 2.9→43.629 Å
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Refine LS restraints |
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LS refinement shell |
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