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- PDB-8yye: Crystal structure of lipase CTL (Caldibacillus Thermoamylovorans) -

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Basic information

Entry
Database: PDB / ID: 8yye
TitleCrystal structure of lipase CTL (Caldibacillus Thermoamylovorans)
Componentstriacylglycerol lipase
KeywordsHYDROLASE / Lipase
Function / homologyDomain of unknown function DUF676, lipase-like / Putative serine esterase (DUF676) / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / triacylglycerol lipase
Function and homology information
Biological speciesCaldibacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsPan, S.Y. / Lan, D.M. / Wang, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of lipase CTL (Caldibacillus Thermoamylovorans)
Authors: Pan, S.Y. / Lan, D.M. / Wang, Y.H.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBC
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: triacylglycerol lipase
B: triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2838
Polymers86,8912
Non-polymers3926
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-117 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.859, 148.965, 58.884
Angle α, β, γ (deg.)90.000, 100.948, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein triacylglycerol lipase


Mass: 43445.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldibacillus thermoamylovorans (bacteria)
Gene: BT1A1_2518 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A090IW71, triacylglycerol lipase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 200 mM zinc acetate, 100 mM sodium acetate/acetic acid (pH 4.9), 11% polyethylene glycol 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.52→57.81 Å / Num. obs: 27750 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 28.46 Å2 / CC1/2: 0.955 / Net I/σ(I): 4.5
Reflection shellResolution: 2.52→2.65 Å / Num. unique obs: 27750 / CC1/2: 0.877

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→40.93 Å / SU ML: 0.303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 1999 7.22 %
Rwork0.1991 25703 -
obs0.2029 27702 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 2.52→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6113 0 6 127 6246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796319
X-RAY DIFFRACTIONf_angle_d0.9128600
X-RAY DIFFRACTIONf_chiral_restr0.0528856
X-RAY DIFFRACTIONf_plane_restr0.00751115
X-RAY DIFFRACTIONf_dihedral_angle_d4.9436849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.35211450.25541856X-RAY DIFFRACTION98.04
2.58-2.650.29531380.23021793X-RAY DIFFRACTION98.72
2.65-2.730.26751440.22011838X-RAY DIFFRACTION98.46
2.73-2.810.28091400.21111807X-RAY DIFFRACTION98.28
2.81-2.910.28351420.2291826X-RAY DIFFRACTION98.8
2.91-3.030.28581430.23631848X-RAY DIFFRACTION98.76
3.03-3.170.33811430.21441824X-RAY DIFFRACTION98.94
3.17-3.340.23741420.21221843X-RAY DIFFRACTION98.76
3.34-3.540.25621420.20831817X-RAY DIFFRACTION98.84
3.54-3.820.25531450.18931867X-RAY DIFFRACTION99.02
3.82-4.20.22271410.17581823X-RAY DIFFRACTION98.79
4.2-4.810.20141440.16521837X-RAY DIFFRACTION99.1
4.81-6.060.22641440.171864X-RAY DIFFRACTION99.36

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