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- PDB-6j1p: Crystal structure of Candida Antarctica Lipase B mutant - SR -

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Basic information

Entry
Database: PDB / ID: 6j1p
TitleCrystal structure of Candida Antarctica Lipase B mutant - SR
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
ACETATE ION / TRIETHYLENE GLYCOL / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 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 9, 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)69,22438
Polymers66,7772
Non-polymers2,44736
Water5,999333
1
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,60920
Polymers33,3891
Non-polymers1,22119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,61518
Polymers33,3891
Non-polymers1,22617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.403, 80.013, 72.968
Angle α, β, γ (deg.)90.00, 97.96, 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 , 6 types, 369 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M ammonium sulfate 32% PEG 4000 0.1 M sodium acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.759→50 Å / Num. obs: 52265 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.062
Reflection shellResolution: 1.759→1.79 Å / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2 / Num. unique obs: 2600

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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: 1.759→36.815 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 2517 5.1 %
Rwork0.18 --
obs0.1814 49330 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.759→36.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 136 333 5127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044921
X-RAY DIFFRACTIONf_angle_d0.8246726
X-RAY DIFFRACTIONf_dihedral_angle_d13.452926
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.007871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7594-1.79320.34371040.26481723X-RAY DIFFRACTION63
1.7932-1.82980.26791040.24712021X-RAY DIFFRACTION73
1.8298-1.86960.28081300.23052276X-RAY DIFFRACTION83
1.8696-1.91310.26751360.21872395X-RAY DIFFRACTION88
1.9131-1.96090.23721400.22022574X-RAY DIFFRACTION93
1.9609-2.01390.2431200.21992664X-RAY DIFFRACTION96
2.0139-2.07320.23171580.20742671X-RAY DIFFRACTION98
2.0732-2.14010.2541540.20452740X-RAY DIFFRACTION100
2.1401-2.21660.2331440.1962782X-RAY DIFFRACTION100
2.2166-2.30530.24481460.192764X-RAY DIFFRACTION100
2.3053-2.41020.23521330.19192758X-RAY DIFFRACTION100
2.4102-2.53730.23421340.18792753X-RAY DIFFRACTION100
2.5373-2.69620.21471470.18762779X-RAY DIFFRACTION100
2.6962-2.90430.24831550.18862773X-RAY DIFFRACTION100
2.9043-3.19640.21541490.1832754X-RAY DIFFRACTION100
3.1964-3.65860.17451630.1632768X-RAY DIFFRACTION100
3.6586-4.6080.16041470.13622787X-RAY DIFFRACTION100
4.608-36.82350.14341530.15212831X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 76.0672 Å / Origin y: -2.9662 Å / Origin z: 33.0967 Å
111213212223313233
T0.1293 Å20.0251 Å20.0191 Å2-0.1379 Å20.0064 Å2--0.1626 Å2
L0.5649 °20.6989 °20.8237 °2-0.7207 °20.8761 °2--1.4834 °2
S0.1657 Å °-0.0655 Å °-0.1179 Å °0.1463 Å °0.0342 Å °-0.1335 Å °0.1703 Å °-0.0679 Å °-0.1358 Å °
Refinement TLS groupSelection details: all

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