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- PDB-6wch: 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: 6wch | ||||||
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Title | Crystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposited dose 7.75 MGy) | ||||||
![]() | Laccase![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Miranda-Blancas, R. / Rudino-Pinera, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.2 KB | Display | ![]() |
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PDB format | ![]() | 84.2 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 | ChemComp-PG4 / ![]() | ||||
#3: Chemical | ![]() #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: 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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 1.7→39.36 Å / Num. obs: 51736 / % possible obs: 99.95 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.058 / Rrim(I) all: 0.0833 / Net I/σ(I): 7.27 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5145 / CC1/2: 0.695 / Rpim(I) all: 0.357 / Rrim(I) all: 0.505 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2XU9 Resolution: 1.7→27.23 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.14 Å2 / Biso mean: 20.5196 Å2 / Biso min: 5.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→27.23 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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