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- PDB-6j1s: Crystal structure of Candida Antarctica Lipase B mutant - SS -

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Basic information

Entry
Database: PDB / ID: 6j1s
TitleCrystal structure of Candida Antarctica Lipase B mutant - SS
ComponentsLipase B
KeywordsHYDROLASE / Calb
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCen, Y.X. / Zhou, J.H. / Wu, Q.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Stereodivergent Protein Engineering of a Lipase To Access All Possible Stereoisomers of Chiral Esters with Two Stereocenters.
Authors: Xu, J. / Cen, Y. / Singh, W. / Fan, J. / Wu, L. / Lin, X. / Zhou, J. / Huang, M. / Reetz, M.T. / Wu, Q.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase B
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0708
Polymers66,5512
Non-polymers5186
Water4,846269
1
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5744
Polymers33,2761
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-11 kcal/mol
Surface area12080 Å2
MethodPISA
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4964
Polymers33,2761
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-19 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.998, 80.417, 73.167
Angle α, β, γ (deg.)90.00, 98.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase B / CALB


Mass: 33275.629 Da / Num. of mol.: 2 / Mutation: T57A, A89T, W104V, D134L, I189M, V190C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate 0.1 M sodium citrate pH 5.5 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50449 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.682
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.24 / Num. unique obs: 2274

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.83→40.208 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.49
RfactorNum. reflection% reflection
Rfree0.2194 2321 5.1 %
Rwork0.188 --
obs0.1896 45510 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→40.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 30 269 4937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014822
X-RAY DIFFRACTIONf_angle_d1.146620
X-RAY DIFFRACTIONf_dihedral_angle_d13.6372916
X-RAY DIFFRACTIONf_chiral_restr0.064770
X-RAY DIFFRACTIONf_plane_restr0.009868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.86740.24961130.21482040X-RAY DIFFRACTION77
1.8674-1.9080.27261120.2152133X-RAY DIFFRACTION81
1.908-1.95240.29851220.21512249X-RAY DIFFRACTION86
1.9524-2.00120.23491210.21042433X-RAY DIFFRACTION92
2.0012-2.05530.24351380.20742514X-RAY DIFFRACTION95
2.0553-2.11580.24541540.21292638X-RAY DIFFRACTION99
2.1158-2.18410.25531260.21212615X-RAY DIFFRACTION100
2.1841-2.26210.26831250.20532679X-RAY DIFFRACTION100
2.2621-2.35270.22871280.20742680X-RAY DIFFRACTION100
2.3527-2.45970.26181410.21262629X-RAY DIFFRACTION100
2.4597-2.58940.2491450.21212643X-RAY DIFFRACTION100
2.5894-2.75160.21861590.21232612X-RAY DIFFRACTION100
2.7516-2.9640.24051490.212653X-RAY DIFFRACTION100
2.964-3.26210.22291590.21552634X-RAY DIFFRACTION100
3.2621-3.73390.21291290.17742671X-RAY DIFFRACTION100
3.7339-4.70310.16951610.13342670X-RAY DIFFRACTION100
4.7031-40.21820.15121390.13822696X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.5184 Å / Origin y: 1.7697 Å / Origin z: 75.6159 Å
111213212223313233
T0.1324 Å2-0.0139 Å20.0394 Å2-0.1435 Å2-0.0084 Å2--0.1219 Å2
L0.5394 °2-0.5824 °20.6919 °2-0.7944 °2-0.7915 °2--0.9982 °2
S0.1418 Å °0.073 Å °-0.0586 Å °-0.1427 Å °-0.0276 Å °0.0735 Å °0.1689 Å °0.0842 Å °-0.0858 Å °
Refinement TLS groupSelection details: all

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