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Yorodumi- PDB-5k3k: Crystal structure of laccase from Thermus thermophilus HB27 (CuSO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k3k | ||||||
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Title | Crystal structure of laccase from Thermus thermophilus HB27 (CuSO4, 20 min) | ||||||
Components | Laccase | ||||||
Keywords | OXIDOREDUCTASE / multicopper oxidases | ||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 Å | ||||||
Authors | Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Rudino-Pinera, E. | ||||||
Funding support | Mexico, 1items
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Citation | Journal: To be Published Title: Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase Authors: Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Stojanoff, V. / Rudino-Pinera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k3k.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k3k.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 5k3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/5k3k ftp://data.pdbj.org/pub/pdb/validation_reports/k3/5k3k | HTTPS FTP |
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-Related structure data
Related structure data | 5jrrC 5jx9C 5k0dC 5k15C 5k5kC 5k84C 2xu9S 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: 48791.457 Da / Num. of mol.: 1 / Fragment: UNP residues 24-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72HW2, laccase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES, pH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 3, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.644→19.632 Å / Num. obs: 38351 / % possible obs: 99.5 % / Observed criterion σ(I): 3.66 / Redundancy: 4.54 % / Biso Wilson estimate: 11.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.95 |
Reflection shell | Resolution: 1.644→1.8 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.32 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2XU9 Resolution: 1.644→19.632 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.38 / Stereochemistry target values: MLHL
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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: 116.27 Å2 / Biso mean: 15.9591 Å2 / Biso min: 1.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.644→19.632 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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