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Yorodumi- PDB-7rab: Crystal structure of a dodecameric multicopper oxidase from M. hy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rab | ||||||
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Title | Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic lattice | ||||||
Components | multicopper oxidase | ||||||
Keywords | OXIDOREDUCTASE / multicopper oxidase thermophile dodecamer laccase | ||||||
Function / homology | Function and homology information : / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding Similarity search - Function | ||||||
Biological species | Marinithermus hydrothermalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å | ||||||
Authors | Georgiadis, M.M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis. Authors: Paavola, J.L. / Battistin, U. / Ogata, C.M. / Georgiadis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rab.cif.gz | 497 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rab.ent.gz | 403.9 KB | Display | PDB format |
PDBx/mmJSON format | 7rab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rab_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7rab_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7rab_validation.xml.gz | 83.6 KB | Display | |
Data in CIF | 7rab_validation.cif.gz | 117.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/7rab ftp://data.pdbj.org/pub/pdb/validation_reports/ra/7rab | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39424.773 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinithermus hydrothermalis (bacteria) Gene: Marky_0543 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: F2NNS0, laccase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-MG / #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: 2.98 Å3/Da / Density % sol: 58.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 0.1 M HEPES 7.5, 25% PEG 335 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.37623 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.37623 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.915→129.47 Å / Num. obs: 284806 / % possible obs: 99.7 % / Redundancy: 39 % / Biso Wilson estimate: 27.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.028 / Rrim(I) all: 0.173 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.8
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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: 3GDC_A Resolution: 1.92→56.06 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.94 Å2 / Biso mean: 30.3317 Å2 / Biso min: 15.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→56.06 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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