+Open data
-Basic information
Entry | Database: PDB / ID: 6kr0 | ||||||
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Title | Crystal structure of HL homo-diabody | ||||||
Components | HL diabody | ||||||
Keywords | IMMUNE SYSTEM / Diabody | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tanaka, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem Eng J / Year: 2020 Title: Association behavior and control of the quality of cancer therapeutic bispecific diabodies expressed in Escherichia coli Authors: Nakazawa, H. / Onodera-Sugano, T. / Sugiyama, A. / Tanaka, Y. / Hattori, T. / Niide, T. / Ogata, H. / Asano, R. / Kumagai, I. / Umetsu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kr0.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kr0.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kr0_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 6kr0_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 6kr0_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 6kr0_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6kr0 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6kr0 | 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 31132.658 Da / Num. of mol.: 4 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: 2.09 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Tirs-HCl pH 9.0, 0.2 M calcium chloride, 3.25 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.75 Å / Num. obs: 47159 / % possible obs: 100 % / Redundancy: 7.43 % / Rsym value: 0.058 / Net I/σ(I): 27.85 |
Reflection shell | Resolution: 2.3→2.3 Å / Num. unique obs: 3394 / Rsym value: 0.887 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.75 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→45.75 Å
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