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

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Basic information

Entry
Database: PDB / ID: 7ykq
TitleCrystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in apo form
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
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesThermomonospora curvata DSM 43183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 apo form
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triacylglycerol lipase
B: Triacylglycerol lipase
C: Triacylglycerol lipase
D: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)117,7634
Polymers117,7634
Non-polymers00
Water4,954275
1
A: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,4411
Polymers29,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,4411
Polymers29,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,4411
Polymers29,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Triacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,4411
Polymers29,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.251, 63.593, 91.537
Angle α, β, γ (deg.)90.000, 97.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

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

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Triacylglycerol lipase


Mass: 29440.805 Da / Num. of mol.: 4 / Mutation: multiple mutations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata DSM 43183 (bacteria)
Gene: Tcur_1278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1A9G5, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.1M HEPES pH 7.5, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.36-2.448.21.19440390.7910.421.2680.503
2.44-2.5410.21.12740410.8760.3621.1850.52
2.54-2.6611.41.01740550.9060.3111.0640.519
2.66-2.8120.78940610.930.2350.8240.566
2.8-2.9712.60.6140420.9550.1780.6360.655
2.97-3.213.50.44240750.9710.1250.460.824
3.2-3.53130.29440850.970.0850.3061.3
3.53-4.0313.30.20940810.9840.060.2172.033
4.03-5.0813.30.16341200.9810.0460.173.616
5.08-5012.80.16142050.9730.0480.1687.309

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFR

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
RfactorNum. reflection% reflection
Rfree0.2462 2009 5.01 %
Rwork0.2084 38079 -
obs0.2103 40088 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.52 Å2 / Biso mean: 33.2806 Å2 / Biso min: 17.99 Å2
Refinement stepCycle: final / Resolution: 2.36→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 0 275 8231
Biso mean---36.38 -
Num. residues----1036
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3172X-RAY DIFFRACTION6.944TORSIONAL
12B3172X-RAY DIFFRACTION6.944TORSIONAL
13C3172X-RAY DIFFRACTION6.944TORSIONAL
14D3172X-RAY DIFFRACTION6.944TORSIONAL
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 (%)
2.36-2.450.30941720.25423078325080
2.45-2.550.29642030.24438424045100
2.55-2.660.29292040.241438664070100
2.66-2.80.25621970.223938724069100
2.8-2.980.2382030.218138614064100
2.98-3.210.26822030.2239104113100
3.21-3.530.24872050.200138834088100
3.53-4.040.2252050.194339124117100
4.04-5.090.21862030.18339234126100
5.09-45.340.23552140.20623932414698

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