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- PDB-9jcb: CalA-like lipase from Kalmanozyma brasiliensis -

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Basic information

Entry
Database: PDB / ID: 9jcb
TitleCalA-like lipase from Kalmanozyma brasiliensis
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 speciesKalmanozyma brasiliensis GHG001 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.46 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
B: Lipase
C: Lipase
D: Lipase
E: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,25612
Polymers284,9296
Non-polymers1,3276
Water00
1
A: Lipase
B: Lipase
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,1286
Polymers142,4643
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-69 kcal/mol
Surface area42090 Å2
MethodPISA
2
D: Lipase
E: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,1286
Polymers142,4643
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-69 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.372, 178.309, 105.386
Angle α, β, γ (deg.)90.000, 119.240, 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
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 28 - 451 / Label seq-ID: 16 - 439

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: Protein
Lipase


Mass: 47488.102 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kalmanozyma brasiliensis GHG001 (fungus)
Gene: PSEUBRA_SCAF1g00196 / Plasmid: pFAi2 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: V5F2U3, 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.: 6 / 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: 3 Å3/Da / Density % sol: 59.04 % / Mosaicity: 0.31 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: 15% MPD: 5% PEG 4,000: 100 mM Imidazole: pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 3.43→45.98 Å / Num. obs: 44108 / % possible obs: 98 % / Redundancy: 7.1 % / Biso Wilson estimate: 89.12 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.378 / Rpim(I) all: 0.153 / Rrim(I) all: 0.408 / Net I/σ(I): 4.6 / Num. measured all: 312650 / Scaling rejects: 163
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
3.43-3.566.62.0952517438130.5150.8562.2670.781.2
12.84-45.986.30.05355238700.990.0240.05824.797.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.45 Å45.36 Å
Translation3.45 Å45.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.8data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.46→45.36 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 2340 5.36 %
Rwork0.1978 41344 -
obs0.2015 43684 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.94 Å2 / Biso mean: 86.129 Å2 / Biso min: 50.53 Å2
Refinement stepCycle: final / Resolution: 3.46→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19356 0 84 0 19440
Biso mean--108.5 --
Num. residues----2544
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11950X-RAY DIFFRACTION8.117TORSIONAL
12B11950X-RAY DIFFRACTION8.117TORSIONAL
13C11950X-RAY DIFFRACTION8.117TORSIONAL
14D11950X-RAY DIFFRACTION8.117TORSIONAL
15E11950X-RAY DIFFRACTION8.117TORSIONAL
16F11950X-RAY DIFFRACTION8.117TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.46-3.530.4111230.35832178230189
3.53-3.60.33981050.320724682573100
3.6-3.690.3421910.297223792570100
3.69-3.780.31821490.259824402589100
3.78-3.880.32921120.253924552567100
3.88-40.28011210.247724512572100
4-4.120.32131030.244924832586100
4.12-4.270.39451640.21623962560100
4.27-4.440.25061430.199924562599100
4.44-4.640.26041680.186423992567100
4.65-4.890.2091310.168124512582100
4.89-5.20.25341670.174124342601100
5.2-5.60.25631440.180324402584100
5.6-6.160.27851230.17724732596100
6.16-7.050.2451050.161424922597100
7.05-8.870.21711290.133124822611100
8.87-45.360.1891620.152124672629100

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