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Basic information

Entry
Database: PDB / ID: 6fms
TitleIMISX-EP of Se-LspA
Components
  • Globomycin
  • Lipoprotein signal peptidase
KeywordsHYDROLASE / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure / MEMBRANE PROTEIN
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
Globomycin / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Lipoprotein signal peptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHuang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Commun Biol / Year: 2018
Title: In situ serial crystallography for rapid de novo membrane protein structure determination.
Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 2.0Jun 19, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _entity_src_gen.gene_src_strain / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Sep 4, 2019Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 3.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)95,69130
Polymers87,8478
Non-polymers7,84422
Water18010
1
A: Lipoprotein signal peptidase
E: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1018
Polymers21,9622
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-11 kcal/mol
Surface area10140 Å2
MethodPISA
2
B: Lipoprotein signal peptidase
F: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4579
Polymers21,9622
Non-polymers2,4967
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area10190 Å2
MethodPISA
3
C: Lipoprotein signal peptidase
G: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1018
Polymers21,9622
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area9900 Å2
MethodPISA
4
D: Lipoprotein signal peptidase
H: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0315
Polymers21,9622
Non-polymers1,0703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.750, 110.130, 85.990
Angle α, β, γ (deg.)90.00, 97.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 21287.877 Da / Num. of mol.: 4
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: 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 / Source: (synth.) synthetic construct (others) / References: Globomycin
#3: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 35 % PEG 400, 100 mM MES, pH 5.6, and 100 mM ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97858 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 3→46.27 Å / Num. obs: 41032 / % possible obs: 99.9 % / Redundancy: 22.7 % / CC1/2: 0.99 / Rrim(I) all: 0.31 / Net I/σ(I): 9.14
Reflection shellResolution: 3→3.08 Å / Redundancy: 22.7 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 3031 / CC1/2: 0.4 / Rrim(I) all: 3.46 / % possible all: 99.8

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3→46.268 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2709 2058 5.02 %
Rwork0.228 --
obs0.2301 41032 99 %
Refinement stepCycle: LAST / Resolution: 3→46.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 586 10 5462

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