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Yorodumi- PDB-3mly: Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mly | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR29 V3 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kong, X.-P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Conserved structural elements in the V3 crown of HIV-1 gp120. Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mly.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mly.ent.gz | 159.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mly_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 3mly_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 3mly_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 3mly_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mly ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mly | HTTPS FTP |
-Related structure data
Related structure data | 3go1C 3mlrC 3mlsC 3mltC 3mluC 3mlvC 3mlwC 3mlxC 3mlzC 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
#1: Antibody | Mass: 22662.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24468.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Protein/peptide | Mass: 2596.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN. | |
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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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2 M NH4 citrate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2008 Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→500 Å / Num. obs: 96835 / % possible obs: 96.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.4 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.511 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.85 / Phase error: 20.5 / 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 / Bsol: 26.396 Å2 / ksol: 0.342 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→30.511 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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