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- PDB-5n4d: Prolyl oligopeptidase B from Galerina marginata bound to 25mer ma... -

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Basic information

Entry
Database: PDB / ID: 5n4d
TitleProlyl oligopeptidase B from Galerina marginata bound to 25mer macrocyclization substrate - D661A mutant
Components
  • Alpha-amanitin proprotein
  • Prolyl oligopeptidase
KeywordsHYDROLASE / amanitin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / toxin activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
Amanitin/phalloidin toxin / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Amanitin/phalloidin toxin / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-amanitin proprotein 1 / Alpha-amanitin proprotein 1 / Dual function macrocyclase-peptidase POPB
Similarity search - Component
Biological speciesGalerina marginata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsCzekster, C.M. / McMahon, S.A. / Ludewig, H. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council339367 NCB-TNT United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Authors: Czekster, C.M. / Ludewig, H. / McMahon, S.A. / Naismith, J.H.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 8, 2017Group: Atomic model / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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 / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Prolyl oligopeptidase
B: Prolyl oligopeptidase
C: Alpha-amanitin proprotein
D: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,4378
Polymers169,0694
Non-polymers3684
Water26,8781492
1
A: Prolyl oligopeptidase
C: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7194
Polymers84,5352
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-15 kcal/mol
Surface area29240 Å2
MethodPISA
2
B: Prolyl oligopeptidase
D: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7194
Polymers84,5352
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-13 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.040, 114.880, 141.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prolyl oligopeptidase


Mass: 81832.594 Da / Num. of mol.: 2 / Mutation: D661A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galerina marginata (fungus) / Gene: POPB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2E7Q8
#2: Protein/peptide Alpha-amanitin proprotein


Mass: 2701.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Galerina marginata (fungus) / References: UniProt: H2E7Q5, UniProt: A0A067SLB9*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1492 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 28% PEG6000, 100 mM Tris pH 8.3, 90 mM sodium/potassium phosphate, 12.5mM Hexammine cobalt chloride. Crystals were cryoprotected with 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.62→49.52 Å / Num. obs: 204059 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 6.93

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Processing

Software
NameVersionClassification
PHENIX(1.11rc3_2553: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→46.875 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.2337 10067 4.94 %
Rwork0.1982 --
obs0.2 203908 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→46.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11708 0 24 1492 13224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01612202
X-RAY DIFFRACTIONf_angle_d1.416608
X-RAY DIFFRACTIONf_dihedral_angle_d5.6199813
X-RAY DIFFRACTIONf_chiral_restr0.091753
X-RAY DIFFRACTIONf_plane_restr0.012162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.33883350.3396363X-RAY DIFFRACTION100
1.6384-1.65770.37193590.31976375X-RAY DIFFRACTION100
1.6577-1.67790.33543440.30576385X-RAY DIFFRACTION100
1.6779-1.69910.3353320.30496412X-RAY DIFFRACTION100
1.6991-1.72150.30963060.28276435X-RAY DIFFRACTION100
1.7215-1.74510.30443250.276418X-RAY DIFFRACTION100
1.7451-1.770.28223360.25746396X-RAY DIFFRACTION100
1.77-1.79640.2883460.2536383X-RAY DIFFRACTION100
1.7964-1.82450.29753290.24596427X-RAY DIFFRACTION100
1.8245-1.85440.28463170.23446435X-RAY DIFFRACTION100
1.8544-1.88640.28443150.24256443X-RAY DIFFRACTION100
1.8864-1.92070.25983420.22966419X-RAY DIFFRACTION100
1.9207-1.95770.25433210.21256437X-RAY DIFFRACTION100
1.9577-1.99760.24533110.20116441X-RAY DIFFRACTION100
1.9976-2.0410.23123150.19336430X-RAY DIFFRACTION100
2.041-2.08850.22873380.19036443X-RAY DIFFRACTION100
2.0885-2.14080.23873460.19126438X-RAY DIFFRACTION100
2.1408-2.19860.23483770.18716401X-RAY DIFFRACTION100
2.1986-2.26330.22743400.18726436X-RAY DIFFRACTION100
2.2633-2.33640.24763240.1876479X-RAY DIFFRACTION100
2.3364-2.41990.23573530.18286435X-RAY DIFFRACTION100
2.4199-2.51680.23553290.18636474X-RAY DIFFRACTION100
2.5168-2.63130.24143240.19686478X-RAY DIFFRACTION100
2.6313-2.770.21793040.19456542X-RAY DIFFRACTION100
2.77-2.94350.2263550.19326481X-RAY DIFFRACTION100
2.9435-3.17080.23143420.19096499X-RAY DIFFRACTION100
3.1708-3.48980.22053380.17966539X-RAY DIFFRACTION100
3.4898-3.99450.19493320.16496590X-RAY DIFFRACTION100
3.9945-5.03170.17823430.15216612X-RAY DIFFRACTION100
5.0317-46.89430.20763890.1996795X-RAY DIFFRACTION99

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