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- PDB-5n4e: Prolyl oligopeptidase B from Galerina marginata bound to 35mer hy... -

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Basic information

Entry
Database: PDB / ID: 5n4e
TitleProlyl oligopeptidase B from Galerina marginata bound to 35mer hydrolysis and macrocyclization substrate - H698A mutant
Components
  • Alpha-amanitin proprotein
  • Prolyl oligopeptidaseProlyl endopeptidase
KeywordsHYDROLASE / amanitin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form
Function / homology
Function and homology information


prolyl oligopeptidase / toxin activity / serine-type endopeptidase activity / proteolysis
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Prolyl oligopeptidase
B: Prolyl oligopeptidase
C: Alpha-amanitin proprotein
D: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,0765
Polymers178,9844
Non-polymers921
Water16,916939
1
A: Prolyl oligopeptidase
C: Alpha-amanitin proprotein


Theoretical massNumber of molelcules
Total (without water)89,4922
Polymers89,4922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-23 kcal/mol
Surface area28710 Å2
MethodPISA
2
B: Prolyl oligopeptidase
D: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5843
Polymers89,4922
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-20 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.180, 115.000, 141.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPLYSLYSAA6 - 7276 - 727
21TRPTRPLYSLYSBB6 - 7276 - 727
12PHEPHECYSCYSCC2 - 352 - 35
22PHEPHECYSCYSDD2 - 352 - 35

NCS ensembles :
ID
1
2

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Components

#1: Protein Prolyl oligopeptidase / Prolyl endopeptidase


Mass: 85641.797 Da / Num. of mol.: 2 / Mutation: H698A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galerina marginata (fungus) / Gene: POPB / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2E7Q8
#2: Protein/peptide Alpha-amanitin proprotein


Mass: 3850.276 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 27% PEGMME2000, 90 mM Bicine pH 8.7, 100 mM potassium thiocyanate, and 12.5mM Hexammine cobalt chloride. Crystals were cryoprotected with 13% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→31.99 Å / Num. obs: 91770 / % possible obs: 93.4 % / Redundancy: 1.8 % / Net I/σ(I): 2.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→89.23 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.867 / SU B: 20.15 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29547 1690 4.9 %RANDOM
Rwork0.24868 ---
obs0.25096 32664 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.042 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20 Å2
2---2.87 Å20 Å2
3---5.05 Å2
Refinement stepCycle: 1 / Resolution: 2.9→89.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11750 0 6 939 12695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912085
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210806
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.93816418
X-RAY DIFFRACTIONr_angle_other_deg0.865325114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8951474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10924.337581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.341151916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3761555
X-RAY DIFFRACTIONr_chiral_restr0.0680.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022581
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5413.2485923
X-RAY DIFFRACTIONr_mcbond_other1.5343.2485922
X-RAY DIFFRACTIONr_mcangle_it2.6394.8647388
X-RAY DIFFRACTIONr_mcangle_other2.644.8647389
X-RAY DIFFRACTIONr_scbond_it1.3493.3446162
X-RAY DIFFRACTIONr_scbond_other1.3483.3446162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3134.9739031
X-RAY DIFFRACTIONr_long_range_B_refined5.23537.36713745
X-RAY DIFFRACTIONr_long_range_B_other5.23437.36613745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A453680.09
12B453680.09
21C14620.11
22D14620.11
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 114 -
Rwork0.356 2247 -
obs--88.03 %

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