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Yorodumi- PDB-7kqy: Crystal Structure and Characterization of Human Heavy-Chain only ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kqy | ||||||
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Title | Crystal Structure and Characterization of Human Heavy-Chain only Antibodies reveals a novel, stable dimeric structure similar to Monoclonal Antibodies | ||||||
Components | Heavy-Chain only Human Antibodies | ||||||
Keywords | IMMUNE SYSTEM / antibody / human heavy-chain dimer | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 Å | ||||||
Authors | Bahmanjah, S. / Mieczkowski, C. / Yu, Y. / Baker, J. / Raghunathan, G. / Tomazela, D. / Hsieh, M. / Mccoy, M. / Strickland, C. / Fayadat-Dilman, L. | ||||||
Citation | Journal: Antibodies / Year: 2020 Title: Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies. Authors: Mieczkowski, C. / Bahmanjah, S. / Yu, Y. / Baker, J. / Raghunathan, G. / Tomazela, D. / Hsieh, M. / McCoy, M. / Strickland, C. / Fayadat-Dilman, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kqy.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kqy.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kqy_validation.pdf.gz | 505.2 KB | Display | wwPDB validaton report |
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Full document | 7kqy_full_validation.pdf.gz | 586 KB | Display | |
Data in XML | 7kqy_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 7kqy_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/7kqy ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kqy | HTTPS FTP |
-Related structure data
Related structure data | 5vsiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 47410.781 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal) |
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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: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion Details: 0.2 M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 25 % 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: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→114.1 Å / Num. obs: 22757 / % possible obs: 75 % / Redundancy: 2 % / CC1/2: 0.979 / Net I/σ(I): 4.85 |
Reflection shell | Resolution: 2.91→3.02 Å / Num. unique obs: 131 / CC1/2: 0.619 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vsi Resolution: 2.913→114.009 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.13 / Stereochemistry target values: MLHL
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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: 2.913→114.009 Å
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Refine LS restraints |
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