+Open data
-Basic information
Entry | Database: PDB / ID: 6h5y | |||||||||
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Title | PM1 mutant, 7D5 | |||||||||
Components | Laccase | |||||||||
Keywords | PLANT PROTEIN | |||||||||
Function / homology | Cupredoxins - blue copper proteins / Immunoglobulin-like / Sandwich / Mainly Beta / COPPER (II) ION Function and homology information | |||||||||
Biological species | Aspergillus oryzae (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Munoz, I.G. / De Salas, F. / Camarero, S. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: PLoS ONE / Year: 2016 Title: Advanced Synthesis of Conductive Polyaniline Using Laccase as Biocatalyst. Authors: de Salas, F. / Pardo, I. / Salavagione, H.J. / Aza, P. / Amougi, E. / Vind, J. / Martinez, A.T. / Camarero, S. #1: Journal: Cell. Mol. Life Sci. / Year: 2015 Title: Laccase engineering by rational and evolutionary design. Authors: Pardo, I. / Camarero, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h5y.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h5y.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 6h5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h5y_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
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Full document | 6h5y_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 6h5y_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 6h5y_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h5y ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h5y | HTTPS FTP |
-Related structure data
Related structure data | 1gycS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53253.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) Plasmid: uracil-independent ampicillin-resistance shuttle pJRoC30 vector Production host: Saccharomyces cerevisiae (brewer's yeast) / Variant (production host): BJ5465 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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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: 3.23 Å3/Da / Density % sol: 62.23 % / Description: Cubic: 0.07x0.07x0.07 mm |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM NaAc, 200 mM Li2SO4, 20% (v/v) polyethylenglycol 4000 and 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→143.27 Å / Num. obs: 61143 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.99 / Rrim(I) all: 0.227 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2298 / CC1/2: 0.935 / Rrim(I) all: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GYC Resolution: 2.3→82.715 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→82.715 Å
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Refine LS restraints |
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LS refinement shell |
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