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- PDB-7e30: Crystal structure of a novel alpha/beta hydrolase in apo form in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7.0E+30 | ||||||
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Title | Crystal structure of a novel alpha/beta hydrolase in apo form in complex with citrate | ||||||
![]() | alpha/beta hydrolase | ||||||
![]() | HYDROLASE / alpha/beta dehydrogenase | ||||||
Function / homology | CITRIC ACID![]() | ||||||
Biological species | unidentified (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, J. / Han, X. / Zheng, Y.Y. / Liu, W.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase. Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / ...Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / Damborsky, J. / Strodel, B. / Liu, W. / Bornscheuer, U.T. / Wei, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.1 KB | Display | ![]() |
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PDB format | ![]() | 93.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cuvC ![]() 7e31C ![]() 7w66C ![]() 7w69C ![]() 7w6cC ![]() 7w6oC ![]() 7w6qC ![]() 5zrqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 27853.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Plasmid: pET-28a / Production host: ![]() ![]() #2: Chemical | ChemComp-CIT / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % / Mosaicity: 0.353 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG 1500, NaAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 20, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→25 Å / Num. obs: 77551 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 1.026 / Net I/σ(I): 17.1 / Num. measured all: 384676 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZRQ Resolution: 1.56→24.55 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.26 / 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: 89.5 Å2 / Biso mean: 20.1243 Å2 / Biso min: 8.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→24.55 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 / % reflection obs: 100 %
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