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- PDB-9fde: Lipase calB candida antarctica with lysine ligand -

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Basic information

Entry
Database: PDB / ID: 9fde
TitleLipase calB candida antarctica with lysine ligand
Components(Lipase B) x 2
KeywordsHYDROLASE / lipase
Function / homology: / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / LYSINE / Lipase B
Function and homology information
Biological speciesMoesziomyces antarcticus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsJelsch, C. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Lipase calB candida antarctica with lysine ligand
Authors: Jelsch, C. / Favier, F. / Didierjean, C.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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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)66,0654
Polymers65,8822
Non-polymers1832
Water2,324129
1
A: Lipase B


Theoretical massNumber of molelcules
Total (without water)33,0401
Polymers33,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0253
Polymers32,8421
Non-polymers1832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.318, 107.476, 68.235
Angle α, β, γ (deg.)90.000, 90.043, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase B / CALB


Mass: 33040.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moesziomyces antarcticus (fungus) / Production host: Escherichia coli B (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Protein Lipase B / CALB


Mass: 32842.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moesziomyces antarcticus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P41365, triacylglycerol lipase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: Platelet-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Propan-2-ol 40 % (V/V), PEG 8000 18 % (W/V), 100mM Imidazole/HCl pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.980121 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980121 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4317
pseudo-merohedral22-h,-k,l20.5683
ReflectionResolution: 1.87→45.32 Å / Num. obs: 52748 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Net I/σ(I): 8.5
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 2665 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→45.318 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.179 / SU B: 4.023 / SU ML: 0.116 / Average fsc free: 0.9493 / Average fsc work: 0.968 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2571 2058 4.691 %
Rwork0.2049 41809 -
all0.207 --
obs-43867 99.289 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.891 Å2
Baniso -1Baniso -2Baniso -3
1--6.219 Å20 Å23.471 Å2
2---16.929 Å2-0 Å2
3---23.149 Å2
Refinement stepCycle: LAST / Resolution: 1.999→45.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 11 129 4773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174362
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6456600
X-RAY DIFFRACTIONr_angle_other_deg1.3441.56110192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8455640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18123.736182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46915690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4321516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02895
X-RAY DIFFRACTIONr_nbd_refined0.2130.21180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24456
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22422
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.215
X-RAY DIFFRACTIONr_nbd_other0.2170.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.211
X-RAY DIFFRACTIONr_mcbond_it1.7692.3562551
X-RAY DIFFRACTIONr_mcbond_other1.7662.3562550
X-RAY DIFFRACTIONr_mcangle_it2.2623.533191
X-RAY DIFFRACTIONr_mcangle_other2.2623.5313192
X-RAY DIFFRACTIONr_scbond_it1.6592.3972248
X-RAY DIFFRACTIONr_scbond_other1.6592.3972248
X-RAY DIFFRACTIONr_scangle_it2.183.5743408
X-RAY DIFFRACTIONr_scangle_other2.1783.5743408
X-RAY DIFFRACTIONr_lrange_it2.99128.9655495
X-RAY DIFFRACTIONr_lrange_other2.98228.9615489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0510.3381390.2443008X-RAY DIFFRACTION96.5337
2.051-2.1070.3171590.2252977X-RAY DIFFRACTION99.3034
2.107-2.1680.2861160.2212954X-RAY DIFFRACTION99.3849
2.168-2.2350.4641340.5092834X-RAY DIFFRACTION99.1647
2.235-2.3080.6091630.5382698X-RAY DIFFRACTION98.9965
2.308-2.3890.2391160.1922717X-RAY DIFFRACTION99.4035
2.389-2.4790.2381220.182568X-RAY DIFFRACTION99.2986
2.479-2.580.2391300.1952453X-RAY DIFFRACTION99.9613
2.58-2.6940.2721050.1772398X-RAY DIFFRACTION99.3254
2.694-2.8260.2531270.1952313X-RAY DIFFRACTION99.9181
2.826-2.9780.2421350.1972085X-RAY DIFFRACTION99.507
2.978-3.1580.2621050.1952070X-RAY DIFFRACTION100.1381
3.158-3.3760.2321130.1911899X-RAY DIFFRACTION99.5054
3.376-3.6460.206770.1951807X-RAY DIFFRACTION99.7353
3.646-3.9930.225890.1821656X-RAY DIFFRACTION99.8855
3.993-4.4620.17700.1381512X-RAY DIFFRACTION99.8107
4.462-5.1490.166640.1261334X-RAY DIFFRACTION99.5018
5.149-6.2970.222300.1551145X-RAY DIFFRACTION99.4078
6.297-8.8670.138340.128890X-RAY DIFFRACTION99.784
8.867-45.30.19300.141491X-RAY DIFFRACTION98.8615

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