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- PDB-5ovm: Solution structure of lipase binding domain LID1 of foldase from ... -

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Basic information

Entry
Database: PDB / ID: 5ovm
TitleSolution structure of lipase binding domain LID1 of foldase from Pseudomonas aeruginosa
ComponentsLipase chaperone
KeywordsCHAPERONE / Lipase A / Lipase interaction domain 1 / Chaperon / Pseudomonas aeruginosa
Function / homologyLipase chaperone / Proteobacterial lipase chaperone protein / : / lipid catabolic process / unfolded protein binding / protein folding / plasma membrane / Lipase chaperone
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsViegas, A. / Jaeger, K.-E. / Etzkorn, M. / Gohlke, H. / Verma, N. / Dollinger, P. / Kovacic, F.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationJA448 8-1 Germany
German Research FoundationET 103/2-1 Germany
European Commission660258 Germany
German Research FoundationGO 1367/1-1 Germany
CitationJournal: Sci Rep / Year: 2020
Title: Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation.
Authors: Viegas, A. / Dollinger, P. / Verma, N. / Kubiak, J. / Viennet, T. / Seidel, C.A.M. / Gohlke, H. / Etzkorn, M. / Kovacic, F. / Jaeger, K.E.
History
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 26, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / pdbx_nmr_sample_details ...atom_site / pdbx_nmr_sample_details / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _pdbx_nmr_sample_details.contents ..._atom_site.auth_seq_id / _pdbx_nmr_sample_details.contents / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 2.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.2Mar 18, 2020Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 2.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase chaperone


Theoretical massNumber of molelcules
Total (without water)10,1081
Polymers10,1081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipase chaperone / Lipase foldase / Lipase helper protein / Lipase modulator


Mass: 10108.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: lifO, lipB, lipH, PA2863 / Plasmid: pEHTHis19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01725

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CB
191isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 450 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O
Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMLipase-interaction domain 1[U-13C; U-15N]1
900 uMLipase-interaction domain 1[U-13C; U-15N]2
Sample conditionsIonic strength: 20 mM / Label: Conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Cerutti, Cheatham, Darden, Duke, Giese, Gohlke, Goetz, Greene, Homeyer, Izadi, Kovalenko, Lee, LeGrand, Li, Lin, Liu, Luchko, Luo, Mermelstein, Merz, Monard, Nguyen, Omelyan, Onufriev, Pan, Qi, Roe, Roitberg, Sagui, Simmerling, Botello-Smith, Swails, Walker, Wang, Wolf, Wu, Xiao, York and Kollmangeometry optimization
TopSpinBruker Biospindata analysis
AmberCase, Cerutti, Cheatham, Darden, Duke, Giese, Gohlke, Goetz, Greene, Homeyer, Izadi, Kovalenko, Lee, LeGrand, Li, Lin, Liu, Luchko, Luo, Mermelstein, Merz, Monard, Nguyen, Omelyan, Onufriev, Pan, Qi, Roe, Roitberg, Sagui, Simmerling, Botello-Smith, Swails, Walker, Wang, Wolf, Wu, Xiao, York and Kollmanrefinement
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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