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- PDB-5uw3: PCY1 in Complex with Follower Peptide -

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Basic information

Entry
Database: PDB / ID: 5uw3
TitlePCY1 in Complex with Follower Peptide
Components
  • Peptide cyclase 1
  • Presegetalin A1
KeywordsLYASE / Natural Product / Orbitide / Cyclase
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
CACODYLATE ION / Presegetalin A1 / Prolyl endopeptidase
Similarity search - Component
Biological speciesVaccaria hispanica (cowherb)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.
Authors: Chekan, J.R. / Estrada, P. / Covello, P.S. / Nair, S.K.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide cyclase 1
E: Presegetalin A1
B: Peptide cyclase 1
F: Presegetalin A1
C: Peptide cyclase 1
G: Presegetalin A1
D: Peptide cyclase 1
H: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,89612
Polymers350,3488
Non-polymers5484
Water37,1292061
1
A: Peptide cyclase 1
E: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7243
Polymers87,5872
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-0 kcal/mol
Surface area27710 Å2
MethodPISA
2
B: Peptide cyclase 1
F: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7243
Polymers87,5872
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint1 kcal/mol
Surface area28060 Å2
MethodPISA
3
C: Peptide cyclase 1
G: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7243
Polymers87,5872
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-0 kcal/mol
Surface area28500 Å2
MethodPISA
4
D: Peptide cyclase 1
H: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7243
Polymers87,5872
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint0 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.495, 85.591, 137.720
Angle α, β, γ (deg.)87.41, 78.28, 89.33
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: _ / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA - M12 - 103138
21TYRTYRBC - O12 - 103138
12TYRTYRAA - M12 - 103138
22TYRTYRCE - Q12 - 103138
13TYRTYRAA - M12 - 103138
23TYRTYRDG - S12 - 103138
14GLYGLYBC - O5 - 103131
24GLYGLYCE - Q5 - 103131
15THRTHRBC - O3 - 103229
25THRTHRDG - S3 - 103229
16GLYGLYCE - Q5 - 103231
26GLYGLYDG - S5 - 103231

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Peptide cyclase 1


Mass: 85600.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (cowherb) / Gene: Pcy1 / Production host: Escherichia coli (E. coli) / References: UniProt: R4P353
#2: Protein/peptide
Presegetalin A1


Mass: 1986.205 Da / Num. of mol.: 4 / Fragment: UNP residues 14-32 / Source method: obtained synthetically / Source: (synth.) Vaccaria hispanica (cowherb) / References: UniProt: F6LNL5
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2061 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8,000, 0.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 14 mg/mL protein, Protein was preincubated with 5 mM boric acid and 1 mM PSA1 [14-32]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.96→44.9 Å / Num. obs: 201248 / % possible obs: 95.8 % / Redundancy: 3.8 % / Rsym value: 0.129 / Net I/σ(I): 8.9
Reflection shellResolution: 1.96→1.967 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2057 / Rsym value: 0.525 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFS

1qfs


Resolution: 1.96→44.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.122 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22409 9945 4.9 %RANDOM
Rwork0.18892 ---
obs0.19068 191296 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.55 Å20.26 Å2
2---0.45 Å2-0.19 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.96→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22650 0 20 2061 24731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01923248
X-RAY DIFFRACTIONr_bond_other_d0.0090.0221696
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.95231491
X-RAY DIFFRACTIONr_angle_other_deg1.461349991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54552808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29723.9811153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.469153884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25715145
X-RAY DIFFRACTIONr_chiral_restr0.1080.23340
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02126372
X-RAY DIFFRACTIONr_gen_planes_other0.0080.025535
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_it1.8251.78111280
X-RAY DIFFRACTIONr_mcbond_other1.8251.78111279
X-RAY DIFFRACTIONr_mcangle_it2.712.66114072
X-RAY DIFFRACTIONr_mcangle_other2.712.66114073
X-RAY DIFFRACTIONr_scbond_it2.3912.08611968
X-RAY DIFFRACTIONr_scbond_other2.3912.08611969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7293.02317420
X-RAY DIFFRACTIONr_long_range_B_refined6.08115.36327947
X-RAY DIFFRACTIONr_long_range_B_other5.95215.16427186
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)
11A422090.1
12B422090.1
21A420520.11
22C420520.11
31A419170.1
32D419170.1
41B423130.11
42C423130.11
51B425860.1
52D425860.1
61C423770.11
62D423770.11
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 678 -
Rwork0.217 14335 -
obs--96.66 %

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