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Yorodumi- PDB-6ldf: Crystal structure of the Zn-directed tetramer of the engineered c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ldf | ||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96K AB5 | ||||||
Components | engineered cyt cb 562 variant, C96K AB5 | ||||||
Keywords | ELECTRON TRANSPORT / Artificial enzyme / Metallohydrolase / Directed evolution / METAL BINDING PROTEIN | ||||||
Function / homology | HEME C Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Song, W.J. / Yu, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Chem Sci / Year: 2021 Title: Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Authors: Yu, J. / Yang, J. / Seok, C. / Song, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ldf.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ldf.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ldf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ldf_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 6ldf_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6ldf_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6ldf_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/6ldf ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ldf | HTTPS FTP |
-Related structure data
Related structure data | 6ldeC 6ldgC 7dclC 3qi5S 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: Protein | Mass: 11848.258 Da / Num. of mol.: 2 / Mutation: variant, C96K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: 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: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 45% (+/-)-2-methyl-2,4-pentanediol (MPD), 100 mM bis-tris, 200 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→28.62 Å / Num. obs: 9893 / % possible obs: 99.7 % / Redundancy: 39.4 % / Rsym value: 0.108 / Net I/σ(I): 95.02 |
Reflection shell | Resolution: 2.35→2.39 Å / Num. unique obs: 470 / Rsym value: 0.433 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QI5 Resolution: 2.35→28.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.12 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.263 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.45 Å2 / Biso mean: 48.278 Å2 / Biso min: 18.71 Å2
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Refinement step | Cycle: final / Resolution: 2.35→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.354→2.415 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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