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- PDB-9jc9: CalA-like lipase from Ustilago trichophora (S200A mutant) -

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Basic information

Entry
Database: PDB / ID: 9jc9
TitleCalA-like lipase from Ustilago trichophora (S200A mutant)
ComponentsLipase
KeywordsHYDROLASE / alpha/beta-Hydrolases
Function / homologySecretory lipase / Lipase, secreted / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / PALMITIC ACID / Lipase
Function and homology information
Biological speciesUstilago trichophora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsXue, B. / Ling, L.H. / Jia, X. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Acs Sustain Chem Eng / Year: 2025
Title: Sustainable Biosynthesis of Diverse Fatty Acid Esters of Hydroxy Fatty Acids (FAHFAs) for Industrial Production
Authors: Ling, L.H. / Chua, E.T. / Xue, B. / Jia, X. / Chow, J.Y. / Yang, R.L. / Lim, Y.P. / Han, P. / Xie, H. / Tan, C.H. / Nguyen, G.K.T. / Yew, W.S.
History
DepositionAug 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0283
Polymers48,3471
Non-polymers6812
Water3,333185
1
A: Lipase
hetero molecules

A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0566
Polymers96,6942
Non-polymers1,3624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area8490 Å2
ΔGint-40 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.358, 97.358, 209.686
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

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Components

#1: Protein Lipase


Mass: 48347.188 Da / Num. of mol.: 1 / Mutation: S200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago trichophora (fungus) / Strain: Ustilago trichophora / Gene: UTRI_04204_B / Plasmid: pFAi2 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A5C3EAQ1, triacylglycerol lipase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.5 / Details: 0.1M NaOAc trihydrate pH 4.5, 30% v/v PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.37→48.68 Å / Num. obs: 24575 / % possible obs: 99.7 % / Redundancy: 39.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2036 / Net I/σ(I): 20.96
Reflection shellResolution: 2.371→2.456 Å / Rmerge(I) obs: 1.574 / Num. unique obs: 2321 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→48.68 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1260 5.13 %
Rwork0.1944 23310 -
obs0.1965 24570 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.42 Å2 / Biso mean: 40.4586 Å2 / Biso min: 22.77 Å2
Refinement stepCycle: final / Resolution: 2.37→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 46 185 3544
Biso mean--51.34 40.62 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.470.32071160.25772471258797
2.47-2.580.30191520.247525202672100
2.58-2.710.34511450.232425372682100
2.71-2.880.28181320.240725542686100
2.88-3.110.31611440.232825572701100
3.11-3.420.25021450.21325732718100
3.42-3.910.22061400.19126162756100
3.91-4.930.18921440.150226472791100
4.93-48.680.18331420.167828352977100

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