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- PDB-9evi: Crystal structure of candida antarctica lipase B with the putativ... -

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Basic information

Entry
Database: PDB / ID: 9evi
TitleCrystal structure of candida antarctica lipase B with the putative pro-peptide region
ComponentsLipase B
KeywordsLYASE / Lipase B / putative pro-peptide region
Function / homology: / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Lipase B
Function and homology information
Biological speciesMoesziomyces antarcticus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSohail, A.A. / Ruddock, L.W.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland272573 Finland
CitationJournal: To Be Published
Title: Crystal structure of candida antarctica lipase B with the putative pro-peptide region
Authors: Sohail, A.A. / Recacha, R. / Ruddock, L.W.
History
DepositionMar 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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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)68,2638
Polymers67,6162
Non-polymers6466
Water15,223845
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-28 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.344, 80.985, 73.993
Angle α, β, γ (deg.)90.00, 98.30, 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: 33808.191 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 851 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium sodium tartrate tetrahydrate; 0.1 M Bis-Tris propane, pH 7.5; 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.19→54.37 Å / Num. obs: 129759 / % possible obs: 73.5 % / Redundancy: 4.4 % / CC1/2: 0.9989 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 14.5
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 1 % / Rmerge(I) obs: 0.642 / Num. unique obs: 279 / CC1/2: 0.387 / % possible all: 3.03

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→46.85 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1679 4876 5 %
Rwork0.1359 --
obs0.1375 97613 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 42 845 5587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054920
X-RAY DIFFRACTIONf_angle_d0.8126759
X-RAY DIFFRACTIONf_dihedral_angle_d9.16703
X-RAY DIFFRACTIONf_chiral_restr0.064789
X-RAY DIFFRACTIONf_plane_restr0.005889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.27461470.23043106X-RAY DIFFRACTION99
1.47-1.480.27321600.21513092X-RAY DIFFRACTION100
1.48-1.50.23171670.18323017X-RAY DIFFRACTION100
1.5-1.520.22531590.16833098X-RAY DIFFRACTION100
1.52-1.540.21421610.16383087X-RAY DIFFRACTION100
1.54-1.560.19941460.15393097X-RAY DIFFRACTION100
1.56-1.580.24071670.14783096X-RAY DIFFRACTION100
1.58-1.610.17951630.1363041X-RAY DIFFRACTION100
1.61-1.630.17721670.12923100X-RAY DIFFRACTION100
1.63-1.660.18391770.1313036X-RAY DIFFRACTION100
1.66-1.690.17781670.13083117X-RAY DIFFRACTION100
1.69-1.720.20191510.13143061X-RAY DIFFRACTION100
1.72-1.750.20821630.14243081X-RAY DIFFRACTION100
1.75-1.790.1971780.13843046X-RAY DIFFRACTION100
1.79-1.830.2091670.1373105X-RAY DIFFRACTION100
1.83-1.870.19681600.13883074X-RAY DIFFRACTION100
1.87-1.920.18581620.13353111X-RAY DIFFRACTION100
1.92-1.970.17651630.13183075X-RAY DIFFRACTION100
1.97-2.030.15841540.13143093X-RAY DIFFRACTION100
2.03-2.090.17661680.12883079X-RAY DIFFRACTION100
2.09-2.170.17351660.12693100X-RAY DIFFRACTION100
2.17-2.250.17531770.12723099X-RAY DIFFRACTION100
2.25-2.360.14561430.1243087X-RAY DIFFRACTION100
2.36-2.480.16071450.12333138X-RAY DIFFRACTION100
2.48-2.630.16221900.12933069X-RAY DIFFRACTION100
2.63-2.840.14821580.13373098X-RAY DIFFRACTION100
2.84-3.120.18841470.14633157X-RAY DIFFRACTION100
3.12-3.580.15731810.13773065X-RAY DIFFRACTION100
3.58-4.50.14051670.12283127X-RAY DIFFRACTION100
4.51-46.850.13691550.14323185X-RAY DIFFRACTION100

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