+Open data
-Basic information
Entry | Database: PDB / ID: 6yzf | ||||||
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Title | Crystal structure of the M295Y variant of Ssl1 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Laccase / Ssl1 / Cu-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sviceus ATCC 29083 (bacteria) Streptomyces sviceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 Å | ||||||
Authors | Mielenbrink, S. / Olbrich, A. / Urlacher, V. / Span, I. | ||||||
Citation | Journal: To Be Published Title: Effect of the axial ligand mutation on spectral and structural properties of Ssl1 laccase Authors: Mielenbrink, S. / Olbrich, A. / Urlacher, V. / Span, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yzf.cif.gz | 323.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yzf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yzf ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yzf | HTTPS FTP |
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-Related structure data
Related structure data | 6y4aC 6yo5C 6yzdC 6yzyC 4m3hS 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
#1: Protein | Mass: 35650.508 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria) Gene: SSEG_02446 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HSR1 #2: Protein/peptide | | Mass: 372.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Part of the protein chain, but position is unknown / Source: (gene. exp.) Streptomyces sviceus (bacteria) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-CU / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.02 Å3/Da / Density % sol: 39.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM HEPES pH 7.0, 1.4 M ammonium sulfate, 10 mM [Co(NH3)6]Cl3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→49.043 Å / Num. obs: 98807 / % possible obs: 99.3 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 1.684→1.692 Å / Num. unique obs: 4562 / CC1/2: 0.572 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M3H Resolution: 1.684→49.043 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.182 / SU B: 3.077 / SU ML: 0.094 / Average fsc free: 0.8674 / Average fsc work: 0.8793 / Cross valid method: NONE / ESU R: 0.106 / ESU R Free: 0.108 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.684→49.043 Å
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Refine LS restraints |
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LS refinement shell |
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