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- PDB-6ksl: Staphylococcus aureus lipase - S116A inactive mutant -

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Basic information

Entry
Database: PDB / ID: 6ksl
TitleStaphylococcus aureus lipase - S116A inactive mutant
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
YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
butanoic acid / LAURIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKitadokoro, K. / Tanaka, M. / Kamitani, S.
Citation
Journal: Sci Rep / Year: 2020
Title: Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat.
Authors: Kitadokoro, K. / Tanaka, M. / Hikima, T. / Okuno, Y. / Yamamoto, M. / Kamitani, S.
#1: Journal: Sci Rep / Year: 2020
Title: Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat.
Authors: Kitadokoro, K. / Tanaka, M. / Hikima, T. / Okuno, Y. / Yamamoto, M. / Kamitani, S.
#2: Journal: To Be Published
Title: Anti-Obesity drug of Human gastric lipase inhibits pathogenic Staphylococcus aureus lipase.
Authors: Kitadokoro, K. / Tanaka, M. / Kamitani, S.
History
DepositionAug 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)92,55111
Polymers91,5632
Non-polymers9889
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.209, 164.209, 233.053
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipase 2


Mass: 45781.391 Da / Num. of mol.: 2 / Mutation: S116A
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 , 5 types, 21 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsE68Q was genetic variant.

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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: 5.3 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.0M Ammonium phosphate dibasic, 0.1M Tris pH8.5

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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: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 109044 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 65 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 16.8
Reflection shellResolution: 2.59→2.75 Å / Num. unique obs: 17409 / CC1/2: 0.523 / Rrim(I) all: 2.138

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KSI

6ksi


Resolution: 2.59→48.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 2901 5 %RANDOM
Rwork0.2493 55105 --
obs0.2503 58006 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.39 Å2 / Biso mean: 65.5405 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 58 12 6116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196259
X-RAY DIFFRACTIONr_bond_other_d00.025603
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9368471
X-RAY DIFFRACTIONr_angle_other_deg3.93313022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79924.183306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.64915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9511530
X-RAY DIFFRACTIONr_chiral_restr0.1750.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217052
X-RAY DIFFRACTIONr_gen_planes_other0.010.021326
X-RAY DIFFRACTIONr_mcbond_it4.3146.3933054
X-RAY DIFFRACTIONr_mcbond_other4.3126.3923053
X-RAY DIFFRACTIONr_mcangle_it6.29.5853814
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 206 -
Rwork0.409 3902 -
all-4108 -
obs--97.69 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-58.00251.691-1.969
2-64.44563.904-7.812
3-61.98434.1395.925
4-25.54283.759-11.925
5-24.19788.3282.31
6-15.81674.959-26.64
7-47.34371.284-4.324
8-29.12266.105-8.884
9-45.52162.935-8.569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 385
2X-RAY DIFFRACTION2A401
3X-RAY DIFFRACTION3A402
4X-RAY DIFFRACTION4B4 - 385
5X-RAY DIFFRACTION5B401
6X-RAY DIFFRACTION6B402
7X-RAY DIFFRACTION7A501 - 507
8X-RAY DIFFRACTION7B501 - 505
9X-RAY DIFFRACTION8A403
10X-RAY DIFFRACTION8B403 - 404
11X-RAY DIFFRACTION9A404
12X-RAY DIFFRACTION9B405

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