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Yorodumi- PDB-7rdj: Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rdj | |||||||||
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Title | Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN bnAb lineage (non-cysteinylated state) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Immunoglobulin / Broadly Neutralizing / HIV-1 | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Omorodion, O. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Structural and Biochemical Characterization of Cysteinylation in Broadly Neutralizing Antibodies to HIV-1. Authors: Omorodion, O. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rdj.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rdj.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/7rdj ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rdj | HTTPS FTP |
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-Related structure data
Related structure data | 7rdkC 7rdlC 7rdmC 5bzdS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23458.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||||
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#2: Antibody | Mass: 24818.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M disodium tartrate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 32727 / % possible obs: 98.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 22.34 Å2 / CC1/2: 0.8 / Rpim(I) all: 0.1 / Rsym value: 0.14 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1649 / CC1/2: 0.43 / Rpim(I) all: 0.5 / Rsym value: 0.7 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BZD Resolution: 1.93→48.42 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8632 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 25.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→48.42 Å
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Refine LS restraints |
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LS refinement shell |
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