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Yorodumi- PDB-6z0k: Crystal structure of laccase from Pediococcus acidilactici Pp5930... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z0k | |||||||||||||||
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Title | Crystal structure of laccase from Pediococcus acidilactici Pp5930 (Hepes pH 7.5) | |||||||||||||||
Components | Putative multicopper oxidase mco | |||||||||||||||
Keywords | OXIDOREDUCTASE / laccase / multicopper oxidase / lactic acid bacteria | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Pediococcus acidilactici 7_4 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | |||||||||||||||
Authors | Casino, P. / Huesa, J. / Pardo, I. | |||||||||||||||
Funding support | Spain, 4items
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Citation | Journal: Microb Biotechnol / Year: 2021 Title: Structural analysis and biochemical properties of laccase enzymes from two Pediococcus species. Authors: Olmeda, I. / Casino, P. / Collins, R.E. / Sendra, R. / Callejon, S. / Huesa, J. / Soares, A.S. / Ferrer, S. / Pardo, I. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z0k.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z0k.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 6z0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/6z0k ftp://data.pdbj.org/pub/pdb/validation_reports/z0/6z0k | HTTPS FTP |
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-Related structure data
Related structure data | 6xizC 6xj0C 6z0jC 3zdwS 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
#1: Protein | Mass: 54541.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first residue Ala of the sequence found at the PDB belongs to the Histag, that is why it has number 0 Source: (gene. exp.) Pediococcus acidilactici 7_4 (bacteria) Gene: HMPREF9024_01129 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D2EK17 | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 10% PEG8000 10% ethylene glycol 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97927 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→162.49 Å / Num. obs: 45687 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 11.9 / Num. measured all: 304133 / Scaling rejects: 24 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Resolution: 2→2.05 Å
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZDW Resolution: 2→70.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.825 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.137 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.89 Å2 / Biso mean: 30.266 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: final / Resolution: 2→70.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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