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Yorodumi- PDB-6dyk: Iron- and Nitric Oxide-bound structure of the engineered cyt b562... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dyk | |||||||||
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Title | Iron- and Nitric Oxide-bound structure of the engineered cyt b562 variant, CH3Y* | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / Designed protein / 4-helix bundle | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å | |||||||||
Authors | Tezcan, F.A. / Rittle, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Chem. / Year: 2019 Title: An efficient, step-economical strategy for the design of functional metalloproteins. Authors: Rittle, J. / Field, M.J. / Green, M.T. / Tezcan, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dyk.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dyk.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 6dyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dyk ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dyk | HTTPS FTP |
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-Related structure data
Related structure data | 6dy4C 6dy6C 6dy8C 6dybC 6dycC 6dydC 6dyeC 6dyfC 6dygC 6dyhC 6dyiC 6dyjC 6dylC 1m6tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11930.375 Da / Num. of mol.: 4 Mutation: M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABE7 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Drop consists of 2 uL of 25% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 6.0) mixed with 1 uL of 4 mM protein and 2.2 mM Iron(II) Sulfate (Anaerobic crystal growth). ...Details: Drop consists of 2 uL of 25% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 6.0) mixed with 1 uL of 4 mM protein and 2.2 mM Iron(II) Sulfate (Anaerobic crystal growth). Diethylamine NONOate (5 mM) was added to mother liquor prior to crystal harvest |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.73 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.73 Å / Relative weight: 1 |
Reflection | Resolution: 1.955→49.345 Å / Num. obs: 31848 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.955→2.0039 Å / Redundancy: 12 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 3092 / CC1/2: 0.992 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1m6t Resolution: 1.955→49.345 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.955→49.345 Å
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Refine LS restraints |
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LS refinement shell |
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