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- PDB-9g8u: Structure of the LipA:LipB complex from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 9g8u
TitleStructure of the LipA:LipB complex from Acinetobacter baumannii
Components
  • Lactonizing lipase
  • Lipase chaperone
KeywordsLIPID BINDING PROTEIN / lipase / secretion system / bacterial infection / chaperone complex / protein-protein interaction / lipid binding
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / unfolded protein binding / protein folding / plasma membrane
Similarity search - Function
Lipase chaperone / Proteobacterial lipase chaperone protein / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Lipase chaperone / Lactonizing lipase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.174 Å
Authorsde Oliveira Silva, Y.R. / Contreras-Martel, C. / Rodrigues de Melo, R. / Zanphorlin, L. / Trindade, D.M. / Dessen, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/12436-9 and 2018/04344-0 Brazil
CitationJournal: Structure / Year: 2025
Title: Architecture of an embracing lipase-foldase complex of the type II secretion system of Acinetobacter baumannii.
Authors: de Oliveira Silva, Y.R. / Contreras-Martel, C. / Rodrigues de Melo, R. / Zanphorlin, L.M. / Trindade, D.M. / Dessen, A.
History
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactonizing lipase
B: Lipase chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3854
Polymers68,3092
Non-polymers762
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-38 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.686, 133.686, 139.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lactonizing lipase


Mass: 32468.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: DSM 30011 / Gene: lip, HMPREF0010_02549 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: D0CCR9, triacylglycerol lipase
#2: Protein Lipase chaperone / Lipase activator protein / Lipase foldase / Lipase helper protein / Lipase modulator


Mass: 35840.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: DSM 30011 / Gene: lifO, EA706_01485, EA722_01050, P9867_05230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A0J8V187
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.62 % / Description: polyhedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane (pH 7.5), 5% polyethylene glycol (PEG) 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 3.174→48.296 Å / Num. obs: 23444 / % possible obs: 96.2 % / Redundancy: 19 % / CC1/2: 0.997 / Net I/σ(I): 5.57
Reflection shellResolution: 3.174→3.37 Å / Redundancy: 4 % / Num. unique obs: 3992 / CC1/2: 0.214 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS20210323data reduction
XSCALE20210323data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.174→48.296 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.936 / SU B: 48.817 / SU ML: 0.659 / Cross valid method: FREE R-VALUE / ESU R: 1.147 / ESU R Free: 0.456 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.295 1966 8.386 %
Rwork0.2771 21478 -
all0.279 --
obs-23444 94.365 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 151.148 Å2
Baniso -1Baniso -2Baniso -3
1-3.254 Å21.627 Å20 Å2
2--3.254 Å2-0 Å2
3----10.556 Å2
Refinement stepCycle: LAST / Resolution: 3.174→48.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 2 14 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124702
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0010.01266
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.8186368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1215575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.222528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.59210811
X-RAY DIFFRACTIONr_dihedral_angle_6_deg5.36110244
X-RAY DIFFRACTIONr_chiral_restr0.0920.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023654
X-RAY DIFFRACTIONr_nbd_refined0.2560.22289
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2325
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.22
X-RAY DIFFRACTIONr_mcbond_it13.82514.8132306
X-RAY DIFFRACTIONr_mcangle_it21.61126.6392879
X-RAY DIFFRACTIONr_scbond_it15.92215.252396
X-RAY DIFFRACTIONr_scangle_it24.38427.8833489
X-RAY DIFFRACTIONr_lrange_it30.002146.2867463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.174-3.2560.5111100.51915780.51817840.7780.76394.61880.525
3.256-3.3450.471640.46215950.46317650.7360.73699.66010.462
3.345-3.4410.4241270.43715670.43617050.8350.84399.35480.435
3.441-3.5470.4041460.4315140.42716620.8330.8199.87970.425
3.547-3.6620.404910.43910410.43616160.7260.69870.04950.439
3.662-3.790.61900.6049140.60515650.5220.77664.15340.625
3.79-3.9320.5011210.49413200.49515200.8050.81694.80260.509
3.932-4.0920.3381030.37812100.37514560.9080.89190.17860.368
4.092-4.2720.331120.28112810.28513960.9210.93999.78510.256
4.272-4.4790.2851120.24912400.25213530.9260.95399.92610.214
4.479-4.7190.2761040.21911690.22312740.9410.96899.92150.181
4.719-5.0020.299940.20311180.2112130.9440.97399.91760.161
5.002-5.3440.2441170.19710400.20211580.9690.97499.91360.159
5.344-5.7660.2731180.1989460.20710650.9510.97499.90610.158
5.766-6.3070.276840.2289040.2339880.9520.9691000.188
6.307-7.0370.269820.2018290.2079110.9530.9751000.165
7.037-8.0970.236650.1797290.1847940.960.9791000.154
8.097-9.8480.155530.1596410.1586940.9850.9851000.152
9.848-13.6460.215460.1885170.195630.9740.9811000.194
13.646-48.2960.177270.2813250.2723520.9790.9551000.303

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