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Yorodumi- PDB-8aqy: streptavidin mutant S112A with an iridium catalyst for CH activation -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aqy | ||||||
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Title | streptavidin mutant S112A with an iridium catalyst for CH activation | ||||||
Components | Streptavidin | ||||||
Keywords | UNKNOWN FUNCTION / Artificial Metalloenzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Igareta, N.V. / Ward, T.R. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: streptavidin mutant S112A with an iridium catalyst for CH activation Authors: Igareta, N.V. / Ward, T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aqy.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aqy.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 8aqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/8aqy ftp://data.pdbj.org/pub/pdb/validation_reports/aq/8aqy | HTTPS FTP |
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-Related structure data
Related structure data | 3pk2S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16422.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Chemical | ChemComp-NOF / #3: 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES 7.5 pH 10 % w/v PEG 8K 8 % v/v EG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033535183 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000033535183 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.01 Å / Num. obs: 497275 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Num. unique obs: 22922 / CC1/2: 0.712 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3pk2 Resolution: 1.65→46.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.575 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.91 Å2 / Biso mean: 18.693 Å2 / Biso min: 8.37 Å2
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Refinement step | Cycle: final / Resolution: 1.65→46.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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