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Yorodumi- PDB-3mlt: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mlt | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 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 | Function and homology information | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 | 3mlt.cif.gz | 335.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mlt.ent.gz | 281.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mlt ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mlt | HTTPS FTP |
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-Related structure data
Related structure data | 3go1C 3mlrC 3mlsC 3mluC 3mlvC 3mlwC 3mlxC 3mlyC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23331.873 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24191.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Protein/peptide | Mass: 2462.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: Q9WNX3 #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB 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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2 M Na formate, 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: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2007 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: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→50 Å / Num. obs: 62552 / % possible obs: 99.9 % / Rmerge(I) obs: 0.047 / Χ2: 0.335 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→35.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.082 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.863 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.51 Å2 / Biso mean: 44.123 Å2 / Biso min: 11.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→35.74 Å
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LS refinement shell | Resolution: 2.49→2.555 Å / Total num. of bins used: 20
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