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- PDB-7rac: Crystal structure of a dodecameric multicopper oxidase from M. hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rac | ||||||
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Title | Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in an orthorhombic lattice | ||||||
![]() | multicopper oxidase | ||||||
![]() | OXIDOREDUCTASE / multicopper oxidase thermophile dodecamer laccase | ||||||
Function / homology | ![]() : / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Georgiadis, M.M. / Ogata, C.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 755.5 KB | Display | ![]() |
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PDB format | ![]() | 617.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 133.3 KB | Display | |
Data in CIF | ![]() | 189.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39424.773 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Marky_0543 / Production host: ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M CaCl2, 0.1 M Bis-Tris 6.5, 45% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→176.95 Å / Num. obs: 216725 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.056 / Rrim(I) all: 0.207 / Net I/σ(I): 11.8 / Num. measured all: 2933251 / Scaling rejects: 16 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: M. hydrothermalis MCO Resolution: 2.36→61.039 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.32 / 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: 91.82 Å2 / Biso mean: 22.4281 Å2 / Biso min: 6.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→61.039 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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