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Yorodumi- PDB-7dcl: Crystal structure of the Zn-directed tetramer of the engineered c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dcl | ||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I/A38S AB5 | ||||||
Components | engineered cyt cb 562 variant, 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: 2.45 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 | 7dcl.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dcl.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dcl_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 7dcl_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 7dcl_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7dcl_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/7dcl ftp://data.pdbj.org/pub/pdb/validation_reports/dc/7dcl | HTTPS FTP |
-Related structure data
Related structure data | 6ldeC 6ldfC 6ldgC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106
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-Components
#1: Protein | Mass: 11848.235 Da / Num. of mol.: 2 / Mutation: C96I, A38S 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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 21% Polyethylene glycol (PEG) 400, bis-tris, ammonium acetate |
-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 11, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→46.55 Å / Num. obs: 14826 / % possible obs: 99.9 % / Redundancy: 34.2 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.12 / Rsym value: 0.118 / Χ2: 6.04 / Net I/σ(I): 88.55 / Num. measured all: 296066 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QI5 Resolution: 2.45→45.53 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.931 / SU ML: 0.199 / SU R Cruickshank DPI: 0.8138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.814 / ESU R Free: 0.306 / 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: 107.43 Å2 / Biso mean: 37.945 Å2 / Biso min: 19.76 Å2
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Refinement step | Cycle: final / Resolution: 2.45→45.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3257 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.452→2.516 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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