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Yorodumi- PDB-7kbm: Reverse Transcriptase Diabody with R83C Mutation Crystallized in C2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kbm | ||||||
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Title | Reverse Transcriptase Diabody with R83C Mutation 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 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 | 7kbm.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kbm.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kbm_validation.pdf.gz | 415.9 KB | Display | wwPDB validaton report |
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Full document | 7kbm_full_validation.pdf.gz | 417.7 KB | Display | |
Data in XML | 7kbm_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7kbm_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/7kbm ftp://data.pdbj.org/pub/pdb/validation_reports/kb/7kbm | HTTPS FTP |
-Related structure data
Related structure data | 6vrpSC 6vugC 6vunC 6vuoC 6vupC 7kboC 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: 26403.193 Da / Num. of mol.: 1 / Mutation: R83C 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Sodium acetate trihydrate pH 4.5, 30% PEG 300 |
-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→50 Å / Num. obs: 13604 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.19 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.12 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 669 / CC1/2: 0.881 / Rrim(I) all: 0.417 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VRP Resolution: 2→33.38 Å / SU ML: 0.3242 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 30.3003 / 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: 26.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.38 Å
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Refine LS restraints |
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LS refinement shell |
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