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Yorodumi- PDB-4q2z: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q2z | ||||||
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Title | Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment / HIV viral envelope glycoprotein neutralization | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Navis, M. / Tran, K. / Bale, S. / Phad, G. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. ...Navis, M. / Tran, K. / Bale, S. / Phad, G. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. / Li, Y. / Wyatt, R.T. / Hedestam, G.B.K. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization. Authors: Navis, M. / Tran, K. / Bale, S. / Phad, G.E. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. / Li, Y. / 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 | 4q2z.cif.gz | 333 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2z.ent.gz | 270.8 KB | Display | PDB format |
PDBx/mmJSON format | 4q2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q2z_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 4q2z_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 4q2z_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 4q2z_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2z ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2z | HTTPS FTP |
-Related structure data
Related structure data | 4ktdS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25386.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo Sapiens (human) #2: Antibody | Mass: 22528.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo Sapiens (human) #3: 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: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Tri-lithium citrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 18, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→69.62 Å / Num. all: 62555 / Num. obs: 60025 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 33.35 Å2 / Rsym value: 0.045 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2963 / Rsym value: 0.549 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4KTD Resolution: 1.93→36.991 Å / SU ML: 0.29 / σ(F): 1.98 / Phase error: 32.15 / 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: 1.93→36.991 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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