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- PDB-7ykq: Crystal structure of a novel alpha/beta hydrolase mutant from the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ykq | |||||||||
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Title | Crystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in apo form | |||||||||
![]() | Triacylglycerol lipase | |||||||||
![]() | HYDROLASE / plastic / PET / degradation | |||||||||
Function / homology | Platelet-activating factor acetylhydrolase, isoform II / poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / triacylglycerol lipase activity / Alpha/Beta hydrolase fold / periplasmic space / extracellular region / Poly(ethylene terephthalate) hydrolase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Han, X. / Jian, G. / Bornscheuer, U.T. / Wei, R. / Liu, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in apo form Authors: Han, X. / Jian, G. / Bornscheuer, U.T. / Wei, R. / Liu, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
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PDB format | ![]() | 165.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.9 KB | Display | ![]() |
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Full document | ![]() | 474.2 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jfrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 2 - 260 / Label seq-ID: 11 - 269
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Components
#1: Protein | Mass: 29440.805 Da / Num. of mol.: 4 / Mutation: multiple mutations Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Tcur_1278 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.1M HEPES pH 7.5, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→50 Å / Num. obs: 40804 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.309 / Rpim(I) all: 0.092 / Rrim(I) all: 0.322 / Χ2: 1.922 / Net I/σ(I): 3.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1JFR Resolution: 2.36→45.34 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.52 Å2 / Biso mean: 33.2806 Å2 / Biso min: 17.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→45.34 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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