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- PDB-6j1t: Crystal structure of Candida Antarctica Lipase B mutant SR with p... -

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Basic information

Entry
Database: PDB / ID: 6j1t
TitleCrystal structure of Candida Antarctica Lipase B mutant SR with product analogue
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
(2S)-2-phenyl-N-[(1R)-1-phenylethyl]propanamide / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.783 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,77726
Polymers66,7772
Non-polymers2,00024
Water7,062392
1
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28510
Polymers33,3891
Non-polymers8979
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,49116
Polymers33,3891
Non-polymers1,10315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.642, 80.381, 73.299
Angle α, β, γ (deg.)90.00, 98.23, 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: 33388.676 Da / Num. of mol.: 2 / Mutation: T57A, A89T, V190C, A281G, A282V
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, 416 molecules

#2: Chemical ChemComp-B7U / (2S)-2-phenyl-N-[(1R)-1-phenylethyl]propanamide


Mass: 253.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate 32% PEG 4000 0.1 M sodium acetate pH 5.6 2% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 50420 / % possible obs: 99.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 27.205
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.091 / Num. unique obs: 2262

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.783→37.048 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 2557 5.07 %
Rwork0.1732 --
obs0.1746 50387 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.783→37.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 119 392 5169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074917
X-RAY DIFFRACTIONf_angle_d0.9446729
X-RAY DIFFRACTIONf_dihedral_angle_d12.9262935
X-RAY DIFFRACTIONf_chiral_restr0.054772
X-RAY DIFFRACTIONf_plane_restr0.009875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7826-1.81690.43471190.34552182X-RAY DIFFRACTION82
1.8169-1.85390.33651460.27932612X-RAY DIFFRACTION98
1.8539-1.89430.31141400.24142636X-RAY DIFFRACTION99
1.8943-1.93830.25081540.21352666X-RAY DIFFRACTION99
1.9383-1.98680.22871250.20242661X-RAY DIFFRACTION99
1.9868-2.04050.23111220.1992714X-RAY DIFFRACTION99
2.0405-2.10050.22181670.19072629X-RAY DIFFRACTION100
2.1005-2.16830.23821520.18832665X-RAY DIFFRACTION100
2.1683-2.24580.2291310.18042699X-RAY DIFFRACTION100
2.2458-2.33570.20161430.1742690X-RAY DIFFRACTION100
2.3357-2.4420.19971390.18232724X-RAY DIFFRACTION100
2.442-2.57070.23481360.17872682X-RAY DIFFRACTION100
2.5707-2.73170.23161420.18452708X-RAY DIFFRACTION100
2.7317-2.94260.23631410.18542691X-RAY DIFFRACTION100
2.9426-3.23860.2161510.18542687X-RAY DIFFRACTION100
3.2386-3.70680.16571540.16312707X-RAY DIFFRACTION100
3.7068-4.66870.15221460.12952717X-RAY DIFFRACTION100
4.6687-37.05640.15531490.14812760X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.4086 Å / Origin y: -0.4149 Å / Origin z: 39.4979 Å
111213212223313233
T0.1816 Å2-0.0107 Å20.0296 Å2-0.1675 Å2-0.0052 Å2--0.2153 Å2
L0.6682 °2-0.6094 °20.859 °2-0.7252 °2-0.792 °2--1.4605 °2
S0.1572 Å °0.0743 Å °-0.1222 Å °-0.1407 Å °0.0113 Å °0.1202 Å °0.184 Å °0.0638 Å °-0.1413 Å °
Refinement TLS groupSelection details: all

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