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- PDB-9l3c: Staphylococcus aureus lipase-Penfluridol complex (on the ground) -

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Basic information

Entry
Database: PDB / ID: 9l3c
TitleStaphylococcus aureus lipase-Penfluridol complex (on the ground)
ComponentsLipase 2
KeywordsHYDROLASE / fatty acid binding
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Lipase-like, C-terminal domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
UNDECANOIC ACID / HEXANOIC ACID / : / butanoic acid / FORMIC ACID / OCTANOIC ACID (CAPRYLIC ACID) / PROPANOIC ACID / HEPTANOIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKitadokoro, J. / Hirokawa, T. / Kamitani, S. / Kitadokoro, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K10199 Japan
CitationJournal: Sci Rep / Year: 2025
Title: Structural analysis shows the mode of inhibition for Staphylococcus aureus lipase by antipsychotic penfluridol.
Authors: Kitadokoro, J. / Hirokawa, T. / Kamo, M. / Furubayashi, N. / Okuno, Y. / Hikima, T. / Yamamoto, M. / Inaka, K. / Maenaka, K. / Kamitani, S. / Kitadokoro, K.
History
DepositionDec 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 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 2
B: Lipase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,25435
Polymers91,5952
Non-polymers3,66033
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.473, 127.473, 252.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-509-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipase 2


Mass: 45797.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lip, BN1321_80040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1MWF9, triacylglycerol lipase

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Non-polymers , 13 types, 79 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H16O2
#4: Chemical
ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical ChemComp-A1L60 / 1-[4,4-bis(4-fluorophenyl)butyl]-4-[4-chloranyl-3-(trifluoromethyl)phenyl]piperidin-4-ol / Penfluridol


Mass: 523.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27ClF5NO
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-11A / UNDECANOIC ACID


Mass: 186.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22O2 / Comment: antifungal*YM
#12: Chemical ChemComp-SHV / HEPTANOIC ACID


Mass: 130.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H14O2
#13: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.94 Å3/Da / Density % sol: 79.3 % / Description: hexagonal diamond shape
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.8M Sodium Formate, Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 192595 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 2.23→2.37 Å / Redundancy: 13 % / Num. unique obs: 7034 / CC1/2: 0.457 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 13.954 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22441 5068 5 %RANDOM
Rwork0.1899 ---
obs0.19166 96088 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.23→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 234 46 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126420
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165930
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.678663
X-RAY DIFFRACTIONr_angle_other_deg0.5751.58313642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.544530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48210996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027593
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it19.6317.4793058
X-RAY DIFFRACTIONr_mcbond_other19.5637.4733055
X-RAY DIFFRACTIONr_mcangle_it26.12813.4373816
X-RAY DIFFRACTIONr_mcangle_other26.08913.4333815
X-RAY DIFFRACTIONr_scbond_it24.3748.2153362
X-RAY DIFFRACTIONr_scbond_other24.378.2173363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other32.64514.7664848
X-RAY DIFFRACTIONr_long_range_B_refined37.35492.0927757
X-RAY DIFFRACTIONr_long_range_B_other37.35892.0927756
X-RAY DIFFRACTIONr_rigid_bond_restr5.005312350
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.233→2.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 360 -
Rwork0.476 6757 -
obs--96.54 %

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