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- PDB-7ykp: Crystal structure of a novel alpha/beta hydrolase from thermomono... -

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Basic information

Entry
Database: PDB / ID: 7ykp
TitleCrystal structure of a novel alpha/beta hydrolase from thermomonospora curvata with glycerol
ComponentsTriacylglycerol lipase
KeywordsHYDROLASE / plastic / PET / degradation
Function / homologyPlatelet-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
Function and homology information
Biological speciesThermomonospora curvata DSM 43183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsHan, X. / Jian, G. / Bornscheuer, U.T. / Wei, R. / Liu, W.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council China
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Crystal structure of a novel alpha/beta hydrolase from thermomonospora curvata with glycerol
Authors: Han, X. / Jian, G. / Bornscheuer, U.T. / Wei, R. / Liu, W.
History
DepositionJul 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5072
Polymers28,4151
Non-polymers921
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-2 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.630, 71.580, 143.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

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Components

#1: Protein Triacylglycerol lipase


Mass: 28414.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata DSM 43183 (bacteria)
Gene: Tcur_1278 / Production host: Trichoderma reesei QM6a (fungus) / References: UniProt: D1A9G5, triacylglycerol lipase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG 1500, NaAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 74712 / % possible obs: 95.3 % / Redundancy: 8.461 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.077 / Net I/σ(I): 15.34
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 7.889 % / Mean I/σ(I) obs: 3.13 / Num. unique obs: 11136 / CC1/2: 0.91 / % possible all: 89.36

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFR

1jfr


Resolution: 1.18→25.31 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1683 3740 5.01 %
Rwork0.1578 70909 -
obs0.1584 74649 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.89 Å2 / Biso mean: 13.7107 Å2 / Biso min: 4.98 Å2
Refinement stepCycle: final / Resolution: 1.18→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 14 439 2456
Biso mean--22.64 25 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.18-1.220.22093550.21366739709493
1.22-1.270.2273540.19076888724295
1.27-1.330.19233610.18086976733796
1.33-1.40.19233690.1736966733596
1.4-1.490.18813800.16817008738896
1.49-1.60.16783640.15417061742596
1.6-1.760.1713840.1537158754297
1.76-2.020.16413730.15337227760098
2.02-2.540.16543910.15167312770399
2.54-25.310.14944090.14857574798399

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