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- PDB-8k7p: Staphylococcus aureus lipase -PSA complex -

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Basic information

Entry
Database: PDB / ID: 8k7p
TitleStaphylococcus aureus lipase -PSA complex
ComponentsLipase 2
KeywordsHYDROLASE / Lipase Inhibitor complex
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Petroselinic acid / HEXANOIC ACID / ACETIC ACID / butanoic acid / LAURIC ACID / FORMIC ACID / OCTANOIC ACID (CAPRYLIC ACID) / PROPANOIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKitadokoro, J. / Kamitani, S. / Kitadokoro, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Open Bio / Year: 2024
Title: Crystal structure of Staphylococcus aureus lipase complex with unsaturated petroselinic acid.
Authors: Kitadokoro, J. / Kamitani, S. / Okuno, Y. / Hikima, T. / Yamamoto, M. / Hirokawa, T. / Kitadokoro, K.
History
DepositionJul 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)94,89239
Polymers91,5952
Non-polymers3,29737
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.324, 132.324, 248.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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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
Details: E68Q WAS GENETIC VARIANT / 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 , 14 types, 174 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


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


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-4I1 / Petroselinic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#8: Chemical
ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O2
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#14: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Sodium Formate, Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 217650 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rrim(I) all: 0.11 / Net I/σ(I): 9.57
Reflection shellResolution: 2.19→2.32 Å / Redundancy: 6.69 % / Num. unique obs: 35067 / CC1/2: 0.427 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→48.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.691 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21806 5706 5 %RANDOM
Rwork0.19837 ---
obs0.19936 108410 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.962 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--1.36 Å20 Å2
3----2.72 Å2
Refinement stepCycle: 1 / Resolution: 2.19→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 209 142 6399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.678585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6145.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49910996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1530.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024962
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.1885.9493063
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.70510.6523818
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.3716.3173321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.8762.229543
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.244 Å
RfactorNum. reflection% reflection
Rfree0.388 414 -
Rwork0.388 7862 -
obs--99.4 %

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