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- PDB-9emz: 13C/15N-labelled Integral Membrane Enzyme LspA in the Lipid Cubic... -

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Basic information

Entry
Database: PDB / ID: 9emz
Title13C/15N-labelled Integral Membrane Enzyme LspA in the Lipid Cubic Phase
Components
  • Globomycin
  • Lipoprotein signal peptidase
KeywordsHYDROLASE / Lipid Cubic Phase / LspA / Globomycin
Function / homology
Function and homology information


signal peptidase II / signal peptide processing / endopeptidase activity / aspartic-type endopeptidase activity / plasma membrane
Similarity search - Function
Peptidase A8, signal peptidase II / Signal peptidase (SPase) II / Signal peptidases II signature.
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Lipoprotein signal peptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBailey, J. / Boland, C. / Caffrey, M. / Huang, C.-Y. / Gawrisch, K. / Kooshapur, H. / Ramberg, K.O. / Soubias, O. / Wiktor, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 and 22/FFP-A/10278 Ireland
Swiss National Science FoundationP2BSP3_15254 Switzerland
CitationJournal: Biophys.J. / Year: 2025
Title: Solid-state NMR of membrane peptides and proteins in the lipid cubic phase.
Authors: Ramberg, K.O. / Boland, C. / Kooshapur, H. / Soubias, O. / Wiktor, M. / Huang, C.Y. / Bailey, J. / Gawrisch, K. / Caffrey, M.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein signal peptidase
B: Lipoprotein signal peptidase
C: Lipoprotein signal peptidase
D: Lipoprotein signal peptidase
E: Globomycin
F: Globomycin
G: Globomycin
H: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30532
Polymers78,7488
Non-polymers8,55724
Water21612
1
A: Lipoprotein signal peptidase
E: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8268
Polymers19,6872
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein signal peptidase
H: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1839
Polymers19,6872
Non-polymers2,4967
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein signal peptidase
F: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8268
Polymers19,6872
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein signal peptidase
G: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4707
Polymers19,6872
Non-polymers1,7835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.991, 106.086, 85.919
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Lipoprotein signal peptidase / LspPae / Prolipoprotein signal peptidase / Signal peptidase II / SPase II


Mass: 19013.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lspA, ls, PA4559 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HVM5, signal peptidase II
#2: Protein/peptide
Globomycin


Mass: 673.838 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Globomycin / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES pH 5.6-6.0, 35-43 %(v/v) PEG400 and 60-100 mM ammonium phosphate monobasic
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.995→85.176 Å / Num. obs: 10425 / % possible obs: 72.7 % / Redundancy: 2.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
9.94-85.1760.0282.352011
2.995-3.3070.7691.55220.57167.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→60 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3033 525 5.04 %
Rwork0.2453 --
obs0.2484 10410 50.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4945 0 692 12 5649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035750
X-RAY DIFFRACTIONf_angle_d0.6057646
X-RAY DIFFRACTIONf_dihedral_angle_d18.6482068
X-RAY DIFFRACTIONf_chiral_restr0.042841
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.3565290.3345470X-RAY DIFFRACTION10
3.3-3.770.3293730.28531551X-RAY DIFFRACTION32
3.77-4.750.33221760.25133426X-RAY DIFFRACTION70
4.75-600.27532470.22834438X-RAY DIFFRACTION90

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