+Open data
-Basic information
Entry | Database: PDB / ID: 6yzd | ||||||
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Title | Crystal structure of the M295A variant of Ssl1 | ||||||
Components | Copper oxidase | ||||||
Keywords | OXIDOREDUCTASE / Laccase / Ssl1 / Cu-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sviceus ATCC 29083 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 | 6yzd.cif.gz | 312.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yzd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yzd_validation.pdf.gz | 8.1 MB | Display | wwPDB validaton report |
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Full document | 6yzd_full_validation.pdf.gz | 8.1 MB | Display | |
Data in XML | 6yzd_validation.xml.gz | 31 KB | Display | |
Data in CIF | 6yzd_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yzd ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yzd | HTTPS FTP |
-Related structure data
Related structure data | 6y4aC 6yo5C 6yzfC 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: 35558.414 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: Chemical | ChemComp-CU / #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 39.92 % |
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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: May 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→30.36 Å / Num. obs: 168970 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 8312 / CC1/2: 0.621 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M3H Resolution: 1.41→30.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.785 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.065 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.936 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→30.36 Å
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Refine LS restraints |
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LS refinement shell |
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