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- PDB-6ryp: Bacterial membrane enzyme structure by the in meso method at 2.3 ... -

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Basic information

Entry
Database: PDB / ID: 6ryp
TitleBacterial membrane enzyme structure by the in meso method at 2.3 A resolution
ComponentsLipoprotein signal peptidase
KeywordsHYDROLASE / in meso / Lipid cubic phases / lipoprotein signal peptidase / Myxovirescin
Function / homology
Function and homology information


signal peptidase II / aspartic-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Peptidase A8, signal peptidase II / Signal peptidase (SPase) II / Signal peptidases II signature.
Similarity search - Domain/homology
Myxovirescin A / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Lipoprotein signal peptidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, C.Y. / Olatunji, S. / Bailey, J. / Yu, X. / Olieric, V. / Wang, M. / Caffrey, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Nat Commun / Year: 2020
Title: Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin.
Authors: Olatunji, S. / Yu, X. / Bailey, J. / Huang, C.Y. / Zapotoczna, M. / Bowen, K. / Remskar, M. / Muller, R. / Scanlan, E.M. / Geoghegan, J.A. / Olieric, V. / Caffrey, M.
History
DepositionJun 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein signal peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,53719
Polymers21,2281
Non-polymers4,31018
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.170, 54.170, 317.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A--1-

HIS

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21227.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lspA, lsp, SAR1172 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GHN9, signal peptidase II

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Non-polymers , 6 types, 30 molecules

#2: Chemical ChemComp-KNH / Myxovirescin A


Mass: 623.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H61NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES/NaOH pH 6.5, 40 %(v/v) PEG400, 400 mM ammonium fluoride and 80 mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.4 Å / Num. obs: 23038 / % possible obs: 99.9 % / Redundancy: 7.69 % / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 7.69
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1740 / CC1/2: 0.22 / Rrim(I) all: 2.79 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata scaling
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from D_1292102692

Resolution: 2.3→46.4 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.37
RfactorNum. reflection% reflection
Rfree0.2811 1129 4.9 %
Rwork0.2545 --
obs0.2557 23038 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 220 12 1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011520
X-RAY DIFFRACTIONf_angle_d0.3722019
X-RAY DIFFRACTIONf_dihedral_angle_d8.661129
X-RAY DIFFRACTIONf_chiral_restr0.038235
X-RAY DIFFRACTIONf_plane_restr0.002234
LS refinement shellHighest resolution: 2.3 Å
Refinement TLS params.Method: refined / Origin x: -2.9986 Å / Origin y: 15.4438 Å / Origin z: 2.7499 Å
111213212223313233
T0.4864 Å20.0266 Å20.0304 Å2-0.5273 Å20.0169 Å2--0.5886 Å2
L0.9577 °20.0057 °20.5032 °2-2.1118 °2-0.0517 °2--1.5936 °2
S0.0403 Å °0.0467 Å °0.028 Å °-0.044 Å °0.074 Å °-0.0438 Å °-0.2457 Å °0.0077 Å °-0.1138 Å °
Refinement TLS groupSelection details: all

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