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Basic information

Entry
Database: PDB / ID: 7zb1
TitleS580A with 18mer
Components
  • 18mer
  • Prolyl endopeptidase
KeywordsLYASE / macrocyclase for omphalotin A biosynthesis
Function / homologyBICARBONATE ION
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSong, H. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018189/1 United Kingdom
CitationJournal: Biorxiv / Year: 2022
Title: Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides
Authors: Matabaro, E. / Song, H. / Gherlone, F. / Sonderegger, L. / Giltrap, A. / Liver, S. / Gossert, A. / Kunzler, M. / Naismith, J.H.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl endopeptidase
B: Prolyl endopeptidase
C: Prolyl endopeptidase
D: Prolyl endopeptidase
E: 18mer
F: 18mer
G: 18mer
H: 18mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,67633
Polymers345,7248
Non-polymers95225
Water12,286682
1
A: Prolyl endopeptidase
E: 18mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6319
Polymers86,4312
Non-polymers2007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-84 kcal/mol
Surface area29320 Å2
MethodPISA
2
B: Prolyl endopeptidase
F: 18mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5236
Polymers86,4312
Non-polymers924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-48 kcal/mol
Surface area29340 Å2
MethodPISA
3
C: Prolyl endopeptidase
G: 18mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7779
Polymers86,4312
Non-polymers3467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-32 kcal/mol
Surface area28740 Å2
MethodPISA
4
D: Prolyl endopeptidase
H: 18mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7459
Polymers86,4312
Non-polymers3147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-43 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.010, 104.610, 110.650
Angle α, β, γ (deg.)115.810, 98.870, 93.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETHRTHRAA3 - 7313 - 731
21PHEPHETHRTHRBB3 - 7313 - 731
12PROPROGLNGLNAA4 - 7304 - 730
22PROPROGLNGLNCC4 - 7304 - 730
13PROPROTHRTHRAA4 - 7314 - 731
23PROPROTHRTHRDD4 - 7314 - 731
14PROPROMETMETBB4 - 7294 - 729
24PROPROMETMETCC4 - 7294 - 729
15PROPROTHRTHRBB4 - 7314 - 731
25PROPROTHRTHRDD4 - 7314 - 731
16PROPROGLNGLNCC4 - 7304 - 730
26PROPROGLNGLNDD4 - 7304 - 730

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Prolyl endopeptidase / macrocyclase / OphP


Mass: 84445.562 Da / Num. of mol.: 4 / Mutation: S580A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115
#2: Protein/peptide
18mer


Mass: 1985.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 707 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→55.84 Å / Num. obs: 182773 / % possible obs: 98 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.108 / Net I/σ(I): 15
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 1 / Num. unique obs: 8886 / CC1/2: 0.545 / Rrim(I) all: 1.46 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
APEXdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N4C

5n4c


Resolution: 2→55.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.769 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 9445 5.2 %RANDOM
Rwork0.2053 ---
obs0.207 173300 97.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 166.76 Å2 / Biso mean: 45.089 Å2 / Biso min: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å21.21 Å20.6 Å2
2---0.25 Å2-1.28 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 2→55.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23327 0 54 682 24063
Biso mean--63.16 43.18 -
Num. residues----2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01324099
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521787
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.64932683
X-RAY DIFFRACTIONr_angle_other_deg1.2161.57750312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08652900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16221.9351328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98153831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.63415152
X-RAY DIFFRACTIONr_chiral_restr0.0640.23007
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227432
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025808
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235920.07
12B235920.07
21A235810.07
22C235810.07
31A234390.08
32D234390.08
41B237560.07
42C237560.07
51B236720.08
52D236720.08
61C237620.07
62D237620.07
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 666 -
Rwork0.332 12735 -
all-13401 -
obs--96.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4539-0.3805-0.30171.43950.63392.801-0.1461-0.2866-0.32190.21670.4255-0.12680.6540.6382-0.27940.16180.1737-0.08650.5915-0.17820.56484.4092-5.645684.945
23.72931.39410.30610.89990.65130.88210.0191-0.4094-0.22260.1973-0.06830.00450.2652-0.06590.04920.11950.04480.01780.5167-0.1050.4665-33.1708-1.334297.9836
31.95540.3822-2.45721.15770.06724.9648-0.3166-0.1482-0.44640.15320.01010.08760.30920.08820.30650.12990.04020.0990.3003-0.07320.5067-32.7522-15.460383.9826
40.80070.0893-0.6420.80890.67791.5846-0.06810.1303-0.1009-0.0928-0.1510.2098-0.079-0.40760.21920.03280.0285-0.06430.5135-0.23590.5205-35.05772.019369.6698
51.0342-0.2066-0.35790.96040.66681.5635-0.0061-0.19180.0831-0.06080.069-0.0204-0.13450.1878-0.06290.0176-0.0043-0.03790.3543-0.20870.4284-12.854613.878783.3936
61.16810.2157-0.45851.45581.0542.8204-0.1081-0.3375-0.06330.14140.2089-0.07330.36550.4633-0.10070.06510.0942-0.09020.4888-0.18550.4618-4.21752.407392.4814
72.19880.39730.58861.16750.79133.02780.05550.36240.5675-0.09210.0088-0.0456-0.26650.5716-0.06420.0305-0.02860.02490.669-0.00770.9029-10.7528-43.670277.4283
83.30460.3578-0.54591.5224-0.06121.90110.07860.43520.0318-0.1629-0.11810.097-0.163-0.37370.03940.03920.0781-0.06160.6937-0.02160.5583-49.5921-46.404371.0727
91.6475-0.17511.0570.41530.33775.65760.09970.0550.215-0.0049-0.02930.025-0.4124-0.2989-0.07040.08120.1106-0.02160.3794-0.04470.5513-45.7942-35.109685.3231
101.3646-0.47120.03141.350.27811.8045-0.1207-0.1143-0.09490.16760.08830.20450.0739-0.37390.03240.0266-0.00970.01120.5254-0.13450.5674-45.2039-52.5782100.8628
111.2196-0.2974-0.26160.606201.58470.02580.24210.0619-0.0257-0.06410.08760.2972-0.05520.03830.06110.0111-0.00550.4087-0.17210.5226-30.1816-63.398479.5144
121.5870.16320.19760.8249-0.08913.84590.08270.18890.37510.0246-0.0629-0.05370.01270.2816-0.01980.01010.04840.01890.484-0.01350.6183-15.5265-50.435577.1895
132.6117-0.81380.55881.3593-0.190.5222-0.0773-0.07490.1011-0.1762-0.00360.2298-0.1655-0.23980.08090.12040.0119-0.09130.431-0.12820.5083-39.8516-17.4939127.5599
143.0306-0.6810.35212.30440.29753.5917-0.1840.06480.507-0.2431-0.0061-0.0186-0.2414-0.02630.19010.0781-0.0269-0.13520.2732-0.03930.5997-2.8717-11.1039126.0786
151.70330.05521.17731.68120.15050.8963-0.20830.580.0379-0.23550.0351-0.1247-0.17030.26090.17320.0726-0.0871-0.06770.5467-0.14180.5612-9.2677-24.9653111.0593
162.21360.7041-0.85851.1911-1.38162.4043-0.16160.2915-0.477-0.06510.1142-0.06020.14950.080.04740.0191-0.00870.0170.3665-0.22430.6431-2.687-43.6498121.1066
172.0598-0.43220.32380.5086-0.07730.4817-0.1724-0.3977-0.1290.04470.12450.006-0.0325-0.07320.04790.02060.0386-0.04290.4316-0.11240.5094-18.755-28.9967140.3077
182.66830.47310.49032.14771.64372.1564-0.1838-0.18520.1648-0.26080.1541-0.0068-0.13110.11950.02970.06180.0032-0.10070.3676-0.14870.5495-33.7906-15.6797132.7851
191.3892-0.0852-0.67082.47381.15781.3281-0.09370.0757-0.47740.2791-0.2540.56310.1946-0.24060.34770.0471-0.04750.03640.4956-0.24030.6885-27.1016-36.89941.4027
201.1304-0.5432-0.2250.63990.84221.5741-0.1229-0.161-0.26120.17390.1417-0.02290.24880.0726-0.01870.05170.0393-0.00740.3526-0.14280.55445.9749-39.475850.5035
211.3127-0.1591-0.44960.70830.53861.368-0.1575-0.20260.08710.13790.2025-0.1151-0.02620.1998-0.0450.07150.0352-0.04720.4305-0.19690.53663.4609-16.597956.5015
221.2181-0.27950.02890.76480.45920.79510.0150.2759-0.0169-0.1457-0.0222-0.0424-0.1240.01160.00720.0359-0.0315-0.01470.4529-0.17920.46010.5489-23.403727.4667
231.81620.2359-0.03380.85130.70441.0193-0.01130.2155-0.19340.1362-0.1230.24510.029-0.21360.13430.0657-0.0325-0.00850.4805-0.25570.6108-25.2596-27.101537.4657
241.2435-0.828-1.50251.98193.81267.4071-0.26170.0195-0.54170.23080.22770.12020.48840.52240.0340.16030.0016-0.00030.4651-0.22520.6552-16.8487-43.987830.4644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 67
2X-RAY DIFFRACTION2A68 - 147
3X-RAY DIFFRACTION3A148 - 229
4X-RAY DIFFRACTION4A230 - 438
5X-RAY DIFFRACTION5A439 - 649
6X-RAY DIFFRACTION6A650 - 731
7X-RAY DIFFRACTION7B1 - 78
8X-RAY DIFFRACTION8B79 - 146
9X-RAY DIFFRACTION9B147 - 225
10X-RAY DIFFRACTION10B230 - 399
11X-RAY DIFFRACTION11B400 - 630
12X-RAY DIFFRACTION12B631 - 730
13X-RAY DIFFRACTION13C4 - 81
14X-RAY DIFFRACTION14C82 - 169
15X-RAY DIFFRACTION15C170 - 295
16X-RAY DIFFRACTION16C296 - 364
17X-RAY DIFFRACTION17C365 - 656
18X-RAY DIFFRACTION18C657 - 730
19X-RAY DIFFRACTION19D4 - 84
20X-RAY DIFFRACTION20D85 - 229
21X-RAY DIFFRACTION21D230 - 326
22X-RAY DIFFRACTION22D327 - 570
23X-RAY DIFFRACTION23D571 - 697
24X-RAY DIFFRACTION24D698 - 731

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