+Open data
-Basic information
Entry | Database: PDB / ID: 7kbp | ||||||
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Title | Herceptin Diabody with R83T, E85C Mutations | ||||||
Components | Single-chain Fv | ||||||
Keywords | PROTEIN BINDING / diabody / immunoglobin / reverse transcriptase | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chesterman, C. / Arnold, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2021 Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Authors: Chesterman, C. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kbp.cif.gz | 237.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kbp.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 7kbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kbp_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 7kbp_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 7kbp_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 7kbp_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/7kbp ftp://data.pdbj.org/pub/pdb/validation_reports/kb/7kbp | HTTPS FTP |
-Related structure data
Related structure data | 6vrpC 6vugC 6vunC 6vuoC 6vupC 7kbmC 7kboC 4x4xS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 26202.109 Da / Num. of mol.: 4 / Mutation: R83T, E85C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.11 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 9% PEG 550 MME 0.1 M Bicine pH 8.8 |
-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: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 58592 / % possible obs: 99.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.182 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 1.001 / Num. unique obs: 2622 / CC1/2: 0.597 / Rrim(I) all: 1.093 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X4X Resolution: 2.3→49.9 Å / SU ML: 0.2866 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.1902 / Stereochemistry target values: 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: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.9 Å
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Refine LS restraints |
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LS refinement shell |
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