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- PDB-6w9x: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w9x | ||||||
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Title | Crystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposited dose 5.1 MGy) | ||||||
![]() | Laccase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miranda-Blancas, R. / Rudino-Pinera, E. | ||||||
![]() | ![]() Title: Dynamic behavior of alpha-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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.6 KB | Display | ![]() |
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PDB format | ![]() | 84.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xu9S S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-1PE / | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: batch mode / pH: 5.5 / Details: 20% PEG 4000, 20% 2-propanol, 100mM 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing |
Radiation | Monochromator: Si (111) Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→39.24 Å / Num. obs: 51847 / % possible obs: 99.98 % / Redundancy: 8.7 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.75 / CC star: 0.928 / Rmerge(I) obs: 0.7079 / Rpim(I) all: 0.2518 / Rrim(I) all: 0.752 / Net I/σ(I): 55.41 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.266 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 5145 / CC1/2: 0.539 / Rpim(I) all: 0.461 / Rrim(I) all: 1.35 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2XU9 Resolution: 1.7→39.24 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.05 / 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: 129.55 Å2 / Biso mean: 21.2788 Å2 / Biso min: 4.04 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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