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- PDB-6j1q: Crystal structure of Candida Antarctica Lipase B mutant - RS -

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Basic information

Entry
Database: PDB / ID: 6j1q
TitleCrystal structure of Candida Antarctica Lipase B mutant - RS
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: 1.6 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 1.2Nov 6, 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)68,85526
Polymers66,4832
Non-polymers2,37224
Water10,251569
1
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,74916
Polymers33,2411
Non-polymers1,50815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,10610
Polymers33,2411
Non-polymers8649
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.530, 80.449, 72.588
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipase B / CALB


Mass: 33241.480 Da / Num. of mol.: 2 / Mutation: T57A, A89T, W104A, I189V
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

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Non-polymers , 7 types, 593 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate 0.1 M HEPES 7.0 16% PEG 4000 10% isopropanol

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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: 1.6→50 Å / Num. obs: 69637 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 29.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3322

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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: 1.6→46.125 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 3456 5.04 %
Rwork0.1489 --
obs0.1501 68591 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→46.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 145 569 5347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074964
X-RAY DIFFRACTIONf_angle_d1.0266798
X-RAY DIFFRACTIONf_dihedral_angle_d12.23001
X-RAY DIFFRACTIONf_chiral_restr0.056780
X-RAY DIFFRACTIONf_plane_restr0.007886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.62190.2333880.19792103X-RAY DIFFRACTION79
1.6219-1.6450.21451200.19352325X-RAY DIFFRACTION87
1.645-1.66960.21111180.1952458X-RAY DIFFRACTION93
1.6696-1.69570.21131330.18862568X-RAY DIFFRACTION97
1.6957-1.72350.22371350.18742680X-RAY DIFFRACTION99
1.7235-1.75320.231410.18352600X-RAY DIFFRACTION100
1.7532-1.78510.20641600.16552632X-RAY DIFFRACTION100
1.7851-1.81940.19881290.16472647X-RAY DIFFRACTION100
1.8194-1.85660.19371410.1612638X-RAY DIFFRACTION100
1.8566-1.89690.1921630.15542633X-RAY DIFFRACTION100
1.8969-1.94110.18291300.14932648X-RAY DIFFRACTION100
1.9411-1.98960.16891350.14862629X-RAY DIFFRACTION100
1.9896-2.04340.19081330.14512660X-RAY DIFFRACTION100
2.0434-2.10350.17421400.14412643X-RAY DIFFRACTION100
2.1035-2.17140.16021260.14022676X-RAY DIFFRACTION100
2.1714-2.2490.1691460.13872628X-RAY DIFFRACTION100
2.249-2.33910.16851340.13732660X-RAY DIFFRACTION100
2.3391-2.44550.16871540.14362654X-RAY DIFFRACTION100
2.4455-2.57440.15191200.14342674X-RAY DIFFRACTION100
2.5744-2.73570.17341480.14542643X-RAY DIFFRACTION100
2.7357-2.94690.18121410.15212640X-RAY DIFFRACTION100
2.9469-3.24340.17651510.15262668X-RAY DIFFRACTION100
3.2434-3.71260.17131650.13632647X-RAY DIFFRACTION100
3.7126-4.67670.13611510.12272680X-RAY DIFFRACTION100
4.6767-46.14450.15621540.15622701X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.9718 Å / Origin y: 0.4834 Å / Origin z: 2.9038 Å
111213212223313233
T0.0742 Å2-0.0051 Å20.0219 Å2-0.0851 Å2-0.0024 Å2--0.0933 Å2
L0.4057 °2-0.2208 °20.4713 °2-0.2821 °2-0.2949 °2--0.726 °2
S0.0408 Å °0.0563 Å °-0.0221 Å °-0.0312 Å °-0.0102 Å °0.0455 Å °0.0405 Å °0.0647 Å °-0.027 Å °
Refinement TLS groupSelection details: all

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