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- PDB-8gzd: CRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM THERMOMONO... -

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Basic information

Entry
Database: PDB / ID: 8gzd
TitleCRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM THERMOMONOSPORA CURVATA IN APO FORM
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: 1.1 Å
AuthorsHan, X. / Gao, J. / 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 IN APO FORM
Authors: Han, X. / Gao, J. / Bornscheuer, U.T. / Wei, R. / Liu, W.
History
DepositionSep 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)28,4151
Polymers28,4151
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.571, 71.590, 143.079
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-567-

HOH

21A-690-

HOH

31A-722-

HOH

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Components

#1: Protein Triacylglycerol lipase / ALPHA/BETA HYDROLASE


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG4000, 20% glycerol, 0.02 M each amino acid, 0.1 M MES/imidazole pH 6.5

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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: Jan 19, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→26.19 Å / Num. obs: 94978 / % possible obs: 99.5 % / Redundancy: 12.838 % / Biso Wilson estimate: 7.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.189 / Χ2: 0.779 / Net I/σ(I): 11.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.1711.4161.8321.8316932615305148320.7911.91996.9
1.17-1.2513.3511.2123.2919192314375143750.9161.261100
1.25-1.3513.180.8734.9117665913404134040.9570.908100
1.35-1.4712.2730.6077.0315166112357123570.9760.634100
1.47-1.6513.2510.35911.7414861011215112150.9910.374100
1.65-1.913.8470.20717.57137640994099400.9960.215100
1.9-2.3312.9740.12223.64109499844184400.9970.127100
2.33-3.2812.4650.07929.2982507661966190.9980.082100
3.28-26.1913.5740.07136.4851513379837950.9980.07499.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFR

1jfr


Resolution: 1.1→26.19 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 9163 5 %
Rwork0.1822 174109 -
obs0.1826 94909 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.43 Å2 / Biso mean: 12.1805 Å2 / Biso min: 1.93 Å2
Refinement stepCycle: final / Resolution: 1.1→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 422 2418
Biso mean---21.29 -
Num. residues----259
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 (%)
1.1-1.140.38879160.379171451806198
1.14-1.180.2978850.29381744818333100
1.18-1.240.2549630.23871734818311100
1.24-1.30.23318860.22321750218388100
1.3-1.390.21539610.22141738218343100
1.39-1.490.18418900.17631748218372100
1.49-1.640.16788940.15661748218376100
1.64-1.880.17979510.15771743218383100
1.88-2.370.16139100.15341743718347100
2.37-26.190.16089070.15741745118358100

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