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Yorodumi- PDB-3tnm: Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tnm | ||||||
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Title | Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4i antibody / Fab / VIRAL GLYCOPROTEIN GP120 / HIV-1 Env | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Wu, X. / Pazgier, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Diverse specificity and effector function among human antibodies to HIV-1 envelope glycoprotein epitopes exposed by CD4 binding. Authors: Guan, Y. / Pazgier, M. / Sajadi, M.M. / Kamin-Lewis, R. / Al-Darmarki, S. / Flinko, R. / Lovo, E. / Wu, X. / Robinson, J.E. / Seaman, M.S. / Fouts, T.R. / Gallo, R.C. / DeVico, A.L. / Lewis, G.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tnm.cif.gz | 327.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tnm.ent.gz | 277.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tnm_validation.pdf.gz | 465.1 KB | Display | wwPDB validaton report |
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Full document | 3tnm_full_validation.pdf.gz | 477.4 KB | Display | |
Data in XML | 3tnm_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 3tnm_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/3tnm ftp://data.pdbj.org/pub/pdb/validation_reports/tn/3tnm | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 24766.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 22829.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) #3: Chemical | ChemComp-ACT / | #4: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.47 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 10% 2-Propanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 59060 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.107 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2898 / Rsym value: 0.903 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.494 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.123 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.853→1.901 Å / Total num. of bins used: 20
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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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