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- PDB-7zb0: macrocyclase OphP with 15mer -

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Basic information

Entry
Database: PDB / ID: 7zb0
Titlemacrocyclase OphP with 15mer
Components
  • 15mer
  • Prolyl endopeptidase
KeywordsHYDROLASE / macrocyclase for omphalotin A biosynthesis
Function / homologyBICARBONATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 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
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 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: 15mer
F: 15mer
G: 15mer
H: 15mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,00623
Polymers344,2228
Non-polymers78415
Water95553
1
A: Prolyl endopeptidase
E: 15mer


Theoretical massNumber of molelcules
Total (without water)86,0562
Polymers86,0562
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-9 kcal/mol
Surface area29490 Å2
MethodPISA
2
B: Prolyl endopeptidase
F: 15mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1794
Polymers86,0562
Non-polymers1232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area29480 Å2
MethodPISA
3
C: Prolyl endopeptidase
G: 15mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3558
Polymers86,0562
Non-polymers2996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-29 kcal/mol
Surface area29620 Å2
MethodPISA
4
D: Prolyl endopeptidase
H: 15mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4179
Polymers86,0562
Non-polymers3617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-42 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.220, 106.180, 114.790
Angle α, β, γ (deg.)113.040, 101.670, 93.240
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 808
2010B4 - 808
1020A4 - 809
2020C4 - 809
1030A4 - 809
2030D4 - 809
1040B4 - 808
2040C4 - 808
1050B4 - 808
2050D4 - 808
1060C4 - 809
2060D4 - 809

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
15mer


Mass: 1610.034 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, 68 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.47→64.35 Å / Num. obs: 104483 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.142 / Net I/σ(I): 13
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.375 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5186 / CC1/2: 0.53 / Rrim(I) all: 1.618 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N4C

5n4c


Resolution: 2.47→64.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 44.376 / SU ML: 0.391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.126 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5223 5 %RANDOM
Rwork0.2293 ---
obs0.2311 99258 98.58 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 148.28 Å2 / Biso mean: 72.921 Å2 / Biso min: 38.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å21.03 Å2-0.26 Å2
2---0.14 Å21.94 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.47→64.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23176 0 122 53 23351
Biso mean--98.18 61.04 -
Num. residues----2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01323879
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521651
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.64932378
X-RAY DIFFRACTIONr_angle_other_deg1.1841.57649975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61652857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67221.9011315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.755153789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.12515151
X-RAY DIFFRACTIONr_chiral_restr0.060.22983
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025756
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A237990.08
12B237990.08
21A236470.07
22C236470.07
31A238660.08
32D238660.08
41B234570.07
42C234570.07
51B241250.07
52D241250.07
61C235500.08
62D235500.08
LS refinement shellResolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 395 -
Rwork0.373 7283 -
all-7678 -
obs--97.93 %
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)
11.0721-0.1503-0.05330.6131-0.26531.7398-0.12270.0411-0.11730.04930.01960.01190.08430.1480.10310.20950.18270.14530.82740.40250.284611.81980.3454-79.5098
21.7359-0.74430.27361.8771-0.79550.93010.00750.32360.15190.0652-0.2034-0.4059-0.07740.14180.19590.02340.0166-0.05490.4580.4020.6734-9.427327.6501-29.5148
33.41540.246-0.4510.5032-0.11661.205-0.3417-0.95870.6235-0.01850.2033-0.01070.08430.13930.13830.18520.2817-0.04110.84090.03680.4046.26515.198618.109
41.6976-0.0130.32771.2452-0.70340.94040.08730.0604-0.0344-0.1825-0.1621-0.09890.03690.14030.07480.1630.14080.11040.46730.30780.2514-2.941-26.1647-33.5017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 807
2X-RAY DIFFRACTION2B4 - 802
3X-RAY DIFFRACTION3C4 - 805
4X-RAY DIFFRACTION4D4 - 806

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