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Yorodumi- PDB-4rqq: Crystal structure of human Fab PGDM1400, a broadly reactive and p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rqq | ||||||
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Title | Crystal structure of human Fab PGDM1400, a broadly reactive and potent HIV-1 neutralizing antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IgG / anti-HIV-1 antibody / HIV-1 Env trimer | ||||||
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: 3.1 Å | ||||||
Authors | Julien, J.-P. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex. Authors: Sok, D. / van Gils, M.J. / Pauthner, M. / Julien, J.P. / Saye-Francisco, K.L. / Hsueh, J. / Briney, B. / Lee, J.H. / Le, K.M. / Lee, P.S. / Hua, Y. / Seaman, M.S. / Moore, J.P. / Ward, A.B. ...Authors: Sok, D. / van Gils, M.J. / Pauthner, M. / Julien, J.P. / Saye-Francisco, K.L. / Hsueh, J. / Briney, B. / Lee, J.H. / Le, K.M. / Lee, P.S. / Hua, Y. / Seaman, M.S. / Moore, J.P. / Ward, A.B. / Wilson, I.A. / Sanders, R.W. / Burton, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rqq.cif.gz | 267.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rqq.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rqq_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 4rqq_full_validation.pdf.gz | 488.3 KB | Display | |
Data in XML | 4rqq_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 4rqq_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/4rqq ftp://data.pdbj.org/pub/pdb/validation_reports/rq/4rqq | HTTPS FTP |
-Related structure data
Related structure data | 3u1sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | Heterodimer made of light chain and heavy chain |
-Components
#1: Antibody | Mass: 24093.719 Da / Num. of mol.: 3 / Fragment: Fab light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human) #2: Antibody | Mass: 26439.633 Da / Num. of mol.: 3 / Fragment: Fab heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human) |
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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: 2.96 Å3/Da / Density % sol: 58.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.04 M potassium dihydrogen phosphate, 16% w/v polyethylene glycol 8000 and 20% v/v glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97947 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 32022 / Num. obs: 30950 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2832 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U1S Resolution: 3.1→38.809 Å / SU ML: 0.43 / σ(F): 1.45 / Phase error: 25.75 / 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: 3.1→38.809 Å
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Refine LS restraints |
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LS refinement shell |
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