+Open data
-Basic information
Entry | Database: PDB / ID: 7vur | ||||||
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Title | Crystal structure of AlleyCat9 with calcium but no inhibitor | ||||||
Components | AlleyCat | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Artificial / enzyme / calmodulin | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Margheritis, E. / Takahashi, K. / Korendovych, I.V. / Tame, J.R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2022 Title: NMR-guided directed evolution. Authors: Bhattacharya, S. / Margheritis, E.G. / Takahashi, K. / Kulesha, A. / D'Souza, A. / Kim, I. / Yoon, J.H. / Tame, J.R.H. / Volkov, A.N. / Makhlynets, O.V. / Korendovych, I.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vur.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vur.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vur_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7vur_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7vur_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7vur_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/7vur ftp://data.pdbj.org/pub/pdb/validation_reports/vu/7vur | HTTPS FTP |
-Related structure data
Related structure data | 7vucC 7vusC 7vutC 7vuuC 1iwqS S: Starting model for refinement C: citing same article (ref.) |
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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: Protein | Mass: 8505.151 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: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, HEPES pH 7, calcium chloride, sodium chloride |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→12.75 Å / Num. obs: 16079 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 806 / Rpim(I) all: 0.177 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1iwq Resolution: 1.7→12.75 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.1485 Stereochemistry target values: GeoStd + Monomer Library + 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: 12.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→12.75 Å
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Refine LS restraints |
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LS refinement shell |
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