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- PDB-6ksi: Staphylococcus aureus lipase - native -

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Basic information

Entry
Database: PDB / ID: 6ksi
TitleStaphylococcus aureus lipase - native
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
HEXANOIC ACID / butanoic acid / LAURIC ACID / PENTANOIC ACID / OCTANOIC ACID (CAPRYLIC ACID) / PALMITIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKitadokoro, K. / Tanaka, M. / Kamitani, S.
CitationJournal: 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.
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)93,56418
Polymers91,5952
Non-polymers1,97016
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-1 kcal/mol
Surface area32250 Å2
Unit cell
Length a, b, c (Å)129.913, 129.913, 251.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
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 , 9 types, 92 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-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BUA / butanoic acid


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 6.2 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.0M Sodium Formate, 0.1M Sodium 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: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 246153 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.089 / Net I/σ(I): 11.6
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 7.1 % / Num. unique obs: 39648 / CC1/2: 0.481 / Rrim(I) all: 2.566 / % possible all: 99.3

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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: 2hih

2hih


Resolution: 2.08→47.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 6444 5 %RANDOM
Rwork0.231 122411 --
obs0.232 128855 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.41 Å2 / Biso mean: 47.4009 Å2 / Biso min: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.08→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 126 76 6250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0196322
X-RAY DIFFRACTIONr_bond_other_d00.025702
X-RAY DIFFRACTIONr_angle_refined_deg2.8961.9448534
X-RAY DIFFRACTIONr_angle_other_deg4.054313262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64724.183306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71815996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1581530
X-RAY DIFFRACTIONr_chiral_restr0.3230.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217080
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021326
X-RAY DIFFRACTIONr_mcbond_it3.4814.523058
X-RAY DIFFRACTIONr_mcbond_other3.4474.5143053
X-RAY DIFFRACTIONr_mcangle_it4.456.7423816
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 466 -
Rwork0.412 8840 -
all-9306 -
obs--98.75 %
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)
116.61726.32-11.849
263.6635.892-24.215
336.70434.388-28.265
443.2528.273-8.441
537.22535.424-16.631
631.0938.233-34.263
724.68331.896-13.307
841.66827.201-20.461
936.68734.75-28.421
103540.464-14.743
1140.27731.12-16.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 385
2X-RAY DIFFRACTION2B4 - 385
3X-RAY DIFFRACTION3A401
4X-RAY DIFFRACTION3B401
5X-RAY DIFFRACTION4A402
6X-RAY DIFFRACTION4B402
7X-RAY DIFFRACTION5A403
8X-RAY DIFFRACTION5B403
9X-RAY DIFFRACTION6A404 - 405
10X-RAY DIFFRACTION6B404
11X-RAY DIFFRACTION7A501 - 559
12X-RAY DIFFRACTION7B501 - 517
13X-RAY DIFFRACTION8A406
14X-RAY DIFFRACTION8B405
15X-RAY DIFFRACTION9A407
16X-RAY DIFFRACTION9B406
17X-RAY DIFFRACTION10A408
18X-RAY DIFFRACTION11A409
19X-RAY DIFFRACTION11B407

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