+Open data
-Basic information
Entry | Database: PDB / ID: 6dyi | |||||||||
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Title | Co(II)-bound structure of the engineered cyt cb562 variant, H3 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / Designed protein / 4-helix bundle / electron transport | |||||||||
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: 1.964 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 | 6dyi.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dyi.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dyi ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dyi | HTTPS FTP |
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-Related structure data
Related structure data | 6dy4C 6dy6C 6dy8C 6dybC 6dycC 6dydC 6dyeC 6dyfC 6dygC 6dyhC 6dyjC 6dykC 6dylC 2bc5S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 11814.240 Da / Num. of mol.: 1 / Mutation: K59W, I67H, Q71H, T97H, R98C, Y101C 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 |
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-Non-polymers , 5 types, 88 molecules
#2: Chemical | ChemComp-CO / | ||
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#3: Chemical | ChemComp-HEC / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-CA / #6: 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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Drop consists of 1 uL of 25% PEG 5000 MME, 200 mM Calcium Chloride and 0.1 M Tris (pH 8.5) mixed with 1 uL of 5 mM protein and 10 mM Cobalt(II) Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→63.25 Å / Num. obs: 9672 / % possible obs: 99.8 % / Redundancy: 10.7 % / CC1/2: 0.988 / Rmerge(I) obs: 0.139 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.96→2.0874 Å / Redundancy: 11 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 924 / CC1/2: 0.917 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.964→63.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.964→63.25 Å
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Refine LS restraints |
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LS refinement shell |
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