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Yorodumi- PDB-7kbo: Reverse Transcriptase Diabody with S82bC, R83T Mutations Crystall... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kbo | ||||||
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Title | Reverse Transcriptase Diabody with S82bC, R83T Mutations Crystallized in C2 | ||||||
Components | Single-chain scFv | ||||||
Keywords | PROTEIN BINDING / diabody / immunoglobin / reverse transcriptase | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7kbo.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kbo.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kbo_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 7kbo_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 7kbo_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 7kbo_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/7kbo ftp://data.pdbj.org/pub/pdb/validation_reports/kb/7kbo | HTTPS FTP |
-Related structure data
Related structure data | 6vrpSC 6vugC 6vunC 6vuoC 6vupC 7kbmC 7kbpC 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 26417.219 Da / Num. of mol.: 1 / Mutation: S82bC, R83T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | ChemComp-EDO / #3: 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: 1.94 Å3/Da / Density % sol: 36.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 6% v/v Propanol, 0.1 M sodium acetate trihydrate pH 4.5, 26 % PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 10076 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.38 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.107 / Num. unique obs: 493 / CC1/2: 0.989 / Rrim(I) all: 0.128 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VRP Resolution: 2.2→33.73 Å / SU ML: 0.2497 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 24.7842 / 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: 29.18 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.73 Å
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Refine LS restraints |
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LS refinement shell |
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