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- PDB-5dir: membrane protein at 2.8 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5dir
Titlemembrane protein at 2.8 Angstroms
Components
  • Globomycin
  • Lipoprotein signal peptidase
KeywordsHYDROLASE / membrane protein / protease / antibiotic / complex
Function / homology
Function and homology information


signal peptidase II / signal peptide processing / 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: 2.8 Å
AuthorsVogeley, L. / El Arnaout, T. / Bailey, J. / Boland, C. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
CitationJournal: Science / Year: 2016
Title: Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin.
Authors: Vogeley, L. / El Arnaout, T. / Bailey, J. / Stansfeld, P.J. / Boland, C. / Caffrey, M.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
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 / entity ...atom_site / entity / entity_poly / entity_poly_seq / 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_validate_close_contact / 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 / _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_validate_close_contact.auth_asym_id_2 / _struct_conn.pdbx_dist_value / _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 2.1Aug 28, 2019Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
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 / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)95,46632
Polymers86,9098
Non-polymers8,55724
Water28816
1
A: Lipoprotein signal peptidase
E: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8668
Polymers21,7272
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area9770 Å2
MethodPISA
2
B: Lipoprotein signal peptidase
H: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2239
Polymers21,7272
Non-polymers2,4967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area10150 Å2
MethodPISA
3
C: Lipoprotein signal peptidase
F: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8668
Polymers21,7272
Non-polymers2,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area9720 Å2
MethodPISA
4
D: Lipoprotein signal peptidase
G: Globomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5107
Polymers21,7272
Non-polymers1,7835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.480, 105.880, 85.390
Angle α, β, γ (deg.)90.000, 96.920, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEPHEchain AAA2 - 15821 - 177
2ASPASPchain BBB2 - 15621 - 175
3ARGARGchain CCC11 - 15930 - 178
4ARGARGchain DDD11 - 15930 - 178

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Components

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


Mass: 21053.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xHis tag and thrombin site
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: lspA, ls, PA4559 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / 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.: 24
Source method: isolated from a genetically manipulated source
Formula: C21H40O4 / References: signal peptidase II
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.8 / Details: PEG 400, ammonium phosphate / PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9824 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9824 Å / Relative weight: 1
ReflectionResolution: 2.8→44.9 Å / Num. obs: 24069 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 67.7 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.086 / Net I/σ(I): 7.3 / Num. measured all: 86063 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.872.70.7891.5464317330.4240.54295.6
12.52-44.93.90.07820.710392660.9860.04392.6

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Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.9 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1207 5.04 %random
Rwork0.2193 22761 --
obs0.2207 23968 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.17 Å2 / Biso mean: 68.2352 Å2 / Biso min: 33.07 Å2
Refinement stepCycle: final / Resolution: 2.8→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 784 16 5653
Biso mean--82.19 53.06 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045762
X-RAY DIFFRACTIONf_angle_d1.0257686
X-RAY DIFFRACTIONf_chiral_restr0.042841
X-RAY DIFFRACTIONf_plane_restr0.004886
X-RAY DIFFRACTIONf_dihedral_angle_d16.5712032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2705X-RAY DIFFRACTION11.661TORSIONAL
12B2705X-RAY DIFFRACTION11.661TORSIONAL
13C2705X-RAY DIFFRACTION11.661TORSIONAL
14D2705X-RAY DIFFRACTION11.661TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.91220.35061290.30122445X-RAY DIFFRACTION95
2.9122-3.04470.33541350.29462527X-RAY DIFFRACTION97
3.0447-3.20520.30911260.25632496X-RAY DIFFRACTION97
3.2052-3.40590.27521240.23122529X-RAY DIFFRACTION97
3.4059-3.66880.22541250.2262570X-RAY DIFFRACTION99
3.6688-4.03780.24861450.21452551X-RAY DIFFRACTION99
4.0378-4.62150.24121280.20232536X-RAY DIFFRACTION98
4.6215-5.82070.21071610.20742543X-RAY DIFFRACTION99
5.8207-44.90.21881340.19982564X-RAY DIFFRACTION97

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