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- PDB-9jca: CalA-like lipase from Ustilago trichophora -

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Basic information

Entry
Database: PDB / ID: 9jca
TitleCalA-like lipase from Ustilago trichophora
ComponentsLipase
KeywordsHYDROLASE / alpha/beta-Hydrolases
Function / homologySecretory lipase / Lipase, secreted / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / Lipase
Function and homology information
Biological speciesUstilago trichophora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.33 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

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5842
Polymers48,3631
Non-polymers2211
Water00
1
A: Lipase
hetero molecules

A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1694
Polymers96,7262
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5980 Å2
ΔGint-48 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.730, 96.730, 207.397
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Lipase


Mass: 48363.188 Da / Num. of mol.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: 2.9 Å3/Da / Density % sol: 57.52 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 24% v/v PEG 400

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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: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.33→48.37 Å / Num. obs: 8996 / % possible obs: 99.4 % / Redundancy: 37.3 % / Biso Wilson estimate: 95.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.035 / Rrim(I) all: 0.218 / Net I/σ(I): 15.3 / Num. measured all: 335754
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.33-3.5937.91.2686587317370.8930.2031.2852.697.3
8.8-48.3733.70.0421959458110.0070.0435899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.52 Å48.37 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.8data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→48.37 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2974 430 4.81 %
Rwork0.221 8506 -
obs0.2247 8936 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.2 Å2 / Biso mean: 88.0899 Å2 / Biso min: 52.02 Å2
Refinement stepCycle: final / Resolution: 3.33→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 14 0 3337
Biso mean--101.55 --
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.33-3.810.40471430.31962713285699
3.81-4.80.32361370.234328022939100
4.8-48.370.24941500.182129913141100

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