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- PDB-5o3w: Structural characterization of the fast and promiscuous macrocycl... -

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Basic information

Entry
Database: PDB / ID: 5o3w
TitleStructural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin A1
Components
  • Peptide cyclase 1
  • Presegetalin A1
KeywordsHYDROLASE / segetalin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form
Function / homology
Function and homology information


oligopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / metal ion binding / cytosol
Similarity search - Function
: / Prolyl oligopeptidase, N-terminal domain / 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 / 7 Propeller ...: / Prolyl oligopeptidase, N-terminal domain / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Presegetalin A1 / Prolyl endopeptidase
Similarity search - Component
Biological speciesVaccaria hispanica (bladder-soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLudewig, H. / Czekster, C.M. / Bent, A.F. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Union339367 NCB-TNT United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates.
Authors: Ludewig, H. / Czekster, C.M. / Oueis, E. / Munday, E.S. / Arshad, M. / Synowsky, S.A. / Bent, A.F. / Naismith, J.H.
History
DepositionMay 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4May 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 / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Peptide cyclase 1
B: Peptide cyclase 1
C: Peptide cyclase 1
D: Peptide cyclase 1
W: Presegetalin A1
X: Presegetalin A1
Y: Presegetalin A1
Z: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,79312
Polymers343,5538
Non-polymers2414
Water15,205844
1
A: Peptide cyclase 1
W: Presegetalin A1


Theoretical massNumber of molelcules
Total (without water)85,8882
Polymers85,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area30280 Å2
MethodPISA
2
B: Peptide cyclase 1
X: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0094
Polymers85,8882
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-28 kcal/mol
Surface area29170 Å2
MethodPISA
3
C: Peptide cyclase 1
Y: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0094
Polymers85,8882
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-27 kcal/mol
Surface area28920 Å2
MethodPISA
4
D: Peptide cyclase 1
Z: Presegetalin A1


Theoretical massNumber of molelcules
Total (without water)85,8882
Polymers85,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.080, 88.600, 144.950
Angle α, β, γ (deg.)93.00, 99.32, 90.05
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: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 6 - 724 / Label seq-ID: 6 - 724

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Peptide cyclase 1


Mass: 82483.266 Da / Num. of mol.: 4 / Mutation: S562A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Gene: Pcy1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4P353
#2: Protein/peptide
Presegetalin A1


Mass: 3404.907 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6LNL5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% ...Details: PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% (v/v) glycerol were added to reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→77.07 Å / Num. obs: 183511 / % possible obs: 97 % / Redundancy: 1.8 % / Net I/σ(I): 4.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo PCY1

Resolution: 2→77.07 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 15.12 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25625 9515 4.9 %RANDOM
Rwork0.22126 ---
obs0.22296 183511 96.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.259 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å2-0.22 Å2-0.38 Å2
2---0.96 Å2-0.01 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2→77.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23045 0 12 844 23901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01923675
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221482
X-RAY DIFFRACTIONr_angle_refined_deg1.641.95332074
X-RAY DIFFRACTIONr_angle_other_deg2.073349925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88352867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38724.0171180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.936153976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.00715149
X-RAY DIFFRACTIONr_chiral_restr0.1040.23404
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02126464
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025033
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_it1.8351.30411480
X-RAY DIFFRACTIONr_mcbond_other1.8351.30411479
X-RAY DIFFRACTIONr_mcangle_it2.8711.94314325
X-RAY DIFFRACTIONr_mcangle_other2.8711.94314326
X-RAY DIFFRACTIONr_scbond_it1.921.47812195
X-RAY DIFFRACTIONr_scbond_other1.921.47612187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9852.14217731
X-RAY DIFFRACTIONr_long_range_B_refined5.9115.0424679
X-RAY DIFFRACTIONr_long_range_B_other5.91114.99224653
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)
11A443020.07
12B443020.07
21A442060.08
22C442060.08
31A448020.06
32D448020.06
41B463940.06
42C463940.06
51B439400.08
52D439400.08
61C438360.08
62D438360.08
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 689 -
Rwork0.331 13441 -
obs--95.78 %
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)
10.48450.0569-0.01611.0449-0.18542.49930.0052-0.03760.07690.3027-0.00710.0852-0.0514-0.17470.00190.23590.03270.07470.02780.04250.36492.013-55.921-294.943
23.75281.8932.37273.21620.43324.1517-0.07890.24580.3286-0.4720.0614-0.1546-0.2344-0.01130.01750.3460.08650.05160.19360.14460.48788.339-52.193-325.912
31.8835-0.385-0.32591.977-0.36232.21440.1246-0.18950.0062-0.1485-0.08520.30370.1647-0.2224-0.03940.2064-0.01870.00720.09190.03740.3205-12.533-64.033-323.27
41.05450.05490.93231.06540.11062.19060.12990.1077-0.0467-0.1547-0.0315-0.02830.53460.2182-0.09840.39590.09910.03890.03520.03210.2577.565-80.571-321.263
51.02470.0546-0.09151.40660.17361.7943-0.0060.04590.0980.29070.0480.01410.3306-0.061-0.0420.33810.01320.03650.02420.07130.2427.926-68.786-292.278
61.62310.02750.24851.63190.58161.5440.0573-0.2323-0.13770.1614-0.03790.05130.25960.0816-0.01940.09280.02350.04620.08880.13150.326229.964-33.832-299.324
71.232-0.0409-0.46011.9070.16811.5320.06960.0232-0.0888-0.32030.0096-0.0817-0.08630.0434-0.07920.20050.05150.05680.02650.03760.301939.945-34.278-323.975
81.81040.1539-0.68291.11910.45931.68420.07340.22260.0154-0.5375-0.06620.0858-0.3075-0.1271-0.00720.43060.09430.01290.07410.09590.285828.952-15.47-329.54
91.6457-0.1334-0.11091.65210.17661.30440.016-0.12620.02690.06-0.00340.1256-0.0927-0.0465-0.01250.05720.01980.05140.02810.05880.25825.723-17.744-299.425
100.9827-0.0524-0.24981.9521.22572.3394-0.0182-0.2242-0.19320.22540.03180.11620.0826-0.0383-0.01360.13010.00760.0680.07490.11440.315722.834-32.38-293.745
112.0391-0.3166-0.291.90050.87682.01610.00880.25580.1162-0.175-0.01620.0064-0.22910.08840.00740.113-0.03650.02580.08550.11360.3182-6.67-28.838-388.353
121.16480.32440.41942.10370.33981.57830.03180.02760.03660.46830.03-0.20410.1420.0374-0.06180.222-0.039-0.02080.03330.04850.34643.005-27.841-363.684
132.0227-0.26240.81011.42870.36351.73820.0832-0.2097-0.00940.7405-0.0669-0.06560.4105-0.1657-0.01630.5277-0.0785-0.01170.06970.10620.2963-7.637-47.277-358.201
141.7068-0.02010.22131.74290.26571.33710.03170.1148-0.0272-0.04750.01080.07210.1408-0.0116-0.04250.0802-0.03060.02140.03890.05180.2793-10.903-44.985-388.237
150.7959-0.05550.19862.27521.13442.6314-0.06080.19850.1689-0.2150.04390.10970.00420.01670.01690.1121-0.03780.01710.06830.09720.3231-13.631-30.502-394.302
160.5523-0.09790.23611.006-0.48993.0213-0.0340.0394-0.0516-0.24240.00480.085-0.0462-0.19960.02920.2328-0.043-0.01440.03910.03160.38825.408-95.442-392.802
171.47010.4093-0.02891.8981-0.2971.93720.0910.1613-0.05180.1674-0.06150.1856-0.1956-0.179-0.02950.23510.01770.03570.09690.03870.296812.885-87.32-364.584
181.1907-0.0268-0.93931.20420.19842.29730.0919-0.1138-0.00130.2482-0.0249-0.0751-0.5780.2294-0.0670.4558-0.1212-0.00910.04760.04370.261632.656-71.196-365.985
191.0079-0.12570.14711.35620.07892.02860.0333-0.0402-0.0871-0.26070.0080.0154-0.4326-0.1252-0.04120.3661-0.0277-0.00050.0360.06910.259830.609-81.188-395.893
204.7323-0.26960.78822.9617-0.31244.64360.0081-0.2108-0.1451-0.15280.08130.017-0.1139-0.0041-0.08940.2073-0.03910.02840.02290.04280.315437.428-96.847-395.491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 107
2X-RAY DIFFRACTION2A108 - 134
3X-RAY DIFFRACTION3A135 - 290
4X-RAY DIFFRACTION4A291 - 420
5X-RAY DIFFRACTION5A421 - 724
6X-RAY DIFFRACTION6B6 - 110
7X-RAY DIFFRACTION7B111 - 266
8X-RAY DIFFRACTION8B267 - 416
9X-RAY DIFFRACTION9B417 - 679
10X-RAY DIFFRACTION10B680 - 724
11X-RAY DIFFRACTION11C6 - 110
12X-RAY DIFFRACTION12C111 - 262
13X-RAY DIFFRACTION13C263 - 416
14X-RAY DIFFRACTION14C417 - 678
15X-RAY DIFFRACTION15C679 - 724
16X-RAY DIFFRACTION16D6 - 107
17X-RAY DIFFRACTION17D108 - 300
18X-RAY DIFFRACTION18D301 - 422
19X-RAY DIFFRACTION19D423 - 691
20X-RAY DIFFRACTION20D692 - 724

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