+Open data
-Basic information
Entry | Database: PDB / ID: 3qyc | ||||||
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Title | Structure of a dimeric anti-HER2 single domain antibody | ||||||
Components | VH domain of IgG molecule | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin V domain fold / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Baral, T.N. / Chao, S. / Li, S. / Tanha, J. / Arbabai, M. / Wang, S. / Zhang, J. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structure of a Human Single Domain Antibody Dimer Formed through V(H)-V(H) Non-Covalent Interactions. Authors: Baral, T.N. / Chao, S.Y. / Li, S. / Tanha, J. / Arbabi-Ghahroudi, M. / Zhang, J. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qyc.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qyc.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qyc_validation.pdf.gz | 423.4 KB | Display | wwPDB validaton report |
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Full document | 3qyc_full_validation.pdf.gz | 425.3 KB | Display | |
Data in XML | 3qyc_validation.xml.gz | 14 KB | Display | |
Data in CIF | 3qyc_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/3qyc ftp://data.pdbj.org/pub/pdb/validation_reports/qy/3qyc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 15740.417 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: 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: 1.98 Å3/Da / Density % sol: 37.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 20% PEG 6000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 33740 / Num. obs: 33598 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.052 |
Reflection shell | Highest resolution: 1.6 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.052 / Num. unique all: 33598 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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