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Yorodumi- PDB-6wcl: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wcl | ||||||
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Title | Crystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposited dose 12.91 MGy) | ||||||
Components | Laccase | ||||||
Keywords | OXIDOREDUCTASE / open conformation / multicopper oxidase / laccase | ||||||
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 / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Miranda-Blancas, R. / Rudino-Pinera, E. | ||||||
Citation | Journal: To Be Published Title: Dynamic behavior of beta-hairpin loop at laccase of Thermus thermophilus at 1.7 angstroms resolution Authors: Miranda-Blancas, R. / 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 | 6wcl.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wcl.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcl ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcl | HTTPS FTP |
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-Related structure data
Related structure data | 6wcgC 6wcmC 6wcnC 6wcpC 2xu9S 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: 48848.512 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72HW2, laccase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-1PE / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % / Description: triangular shaped sheets |
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Crystal grow | Temperature: 277.15 K / Method: microbatch / pH: 5.5 Details: 20% PEG 4000, 20% 2-propanol, 100 mM citrate buffer PH range: 5.5-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→39.24 Å / Num. obs: 51854 / % possible obs: 99.97 % / Redundancy: 1.9 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.068 / Net I/σ(I): 7.93 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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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: 2XU9 Resolution: 1.7→39.24 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.84 Å2 / Biso mean: 24.2195 Å2 / Biso min: 7.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→39.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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