+Open data
-Basic information
Entry | Database: PDB / ID: 6u3z | ||||||
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Title | Structure of VD20_5A4 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / Antibody / HIV | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / PRASEODYMIUM ION Function and homology information | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99002311102 Å | ||||||
Authors | Dionne, G. / Shapiro, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Exp.Med. / Year: 2020 Title: Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. ...Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. / Villablanca, E.J. / Sundling, C. / Murrell, B. / Mascola, J.R. / Shapiro, L. / Pancera, M. / Martin, M. / Corcoran, M. / Wyatt, R.T. / Karlsson Hedestam, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u3z.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u3z.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 6u3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u3z_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 6u3z_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 6u3z_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 6u3z_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/6u3z ftp://data.pdbj.org/pub/pdb/validation_reports/u3/6u3z | HTTPS FTP |
-Related structure data
Related structure data | 6u9uC 2bx5S 5dd5S 5f9wS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 24666.510 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23171.564 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
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-Non-polymers , 5 types, 291 molecules
#3: Chemical | ChemComp-PR / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG3000, 0.2 M sodium chloride, 0.1 M Tris, pH 7, 0.01 M praseodymium(III) acetate hydrate, cryoprotectant: 26% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2017 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→84.31 Å / Num. obs: 67170 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 37.9199020356 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.065 / Rrim(I) all: 0.117 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.99→2.061 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.198 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 6800 / CC1/2: 0.212 / % possible all: 98.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 5F9W, 5DD5, 2BX5 Resolution: 1.99002311102→84.3040636766 Å / SU ML: 0.274506202631 / Cross valid method: FREE R-VALUE / σ(F): 1.33534688718 / Phase error: 27.1519359668
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.2163183524 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99002311102→84.3040636766 Å
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Refine LS restraints |
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LS refinement shell |
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