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- PDB-7yko: Crystal structure of a novel alpha/beta hydrolase mutant from the... -

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Basic information

Entry
Database: PDB / ID: 7yko
TitleCrystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in complex with pentane-1,5-diol
ComponentsTriacylglycerol lipase
KeywordsHYDROLASE / plastic / PET / degradation
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / triacylglycerol lipase activity / periplasmic space / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
pentane-1,5-diol / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesThermomonospora curvata DSM 43183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 mutant from thermomonospora curvata in complex with pentane-1,5-diol
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
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6233
Polymers28,4151
Non-polymers2082
Water7,566420
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)45.660, 71.600, 143.220
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-792-

HOH

21A-813-

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 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1A9G5, triacylglycerol lipase
#2: Chemical ChemComp-9JE / pentane-1,5-diol


Mass: 104.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 40.28 %
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: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→25.32 Å / Num. obs: 83333 / % possible obs: 99.1 % / Redundancy: 11.84 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.22
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 12721 / % possible all: 94.8

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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: 1.15→25.32 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 4157 4.99 %
Rwork0.169 79067 -
obs0.17 83224 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.88 Å2 / Biso mean: 14.08 Å2 / Biso min: 5.79 Å2
Refinement stepCycle: final / Resolution: 1.15→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 38 420 2454
Biso mean--25.63 25.56 -
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 (%)
1.15-1.190.28844080.26767554796297
1.19-1.240.23733900.231378728262100
1.24-1.30.24254320.21578678299100
1.3-1.360.22173960.197478858281100
1.36-1.450.20644210.186678808301100
1.45-1.560.18534220.169178978319100
1.56-1.720.16884070.159279328339100
1.72-1.970.1654250.160879358360100
1.97-2.480.16014250.154480098434100
2.48-25.320.16244310.151982368667100

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