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- PDB-5uw7: PCY1 Y481F Variant in Complex with Follower Peptide -

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Basic information

Entry
Database: PDB / ID: 5uw7
TitlePCY1 Y481F Variant in Complex with Follower Peptide
Components
  • Peptide cyclase 1
  • Presegetalin A1
KeywordsLYASE / Natural Product / Orbitide / Cyclase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
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 / Methylamine Dehydrogenase; Chain H ...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 / Resolution: 2.37 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 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide cyclase 1
C: Presegetalin A1
B: Peptide cyclase 1
D: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,1665
Polymers175,1424
Non-polymers241
Water63135
1
A: Peptide cyclase 1
C: Presegetalin A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5953
Polymers87,5712
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-13 kcal/mol
Surface area27400 Å2
MethodPISA
2
B: Peptide cyclase 1
D: Presegetalin A1


Theoretical massNumber of molelcules
Total (without water)87,5712
Polymers87,5712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.947, 59.629, 134.164
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A12 - 1032
2010B12 - 1032

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Peptide cyclase 1


Mass: 85584.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Gene: Pcy1 / Production host: Escherichia coli (E. coli) / References: UniProt: R4P353
#2: Protein/peptide Presegetalin A1


Mass: 1986.205 Da / Num. of mol.: 2 / Fragment: UNP residues 14-32 / Source method: obtained synthetically / Source: (synth.) Vaccaria hispanica (bladder-soapwort) / References: UniProt: F6LNL5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3,350, 0.1 M magnesium chloride, 0.1 M HEPES free acid (pH 7.5), 7 mg/mL protein, Protein was preincubated with 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: 1.07814 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07814 Å / Relative weight: 1
ReflectionResolution: 2.37→86.9 Å / Num. obs: 55622 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rsym value: 0.092 / Net I/σ(I): 14
Reflection shellResolution: 2.373→2.381 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 551 / Rsym value: 0.751 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementResolution: 2.37→86.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.082 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.311 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28405 2744 4.9 %RANDOM
Rwork0.23629 ---
obs0.23865 52877 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.422 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å2-0 Å20.06 Å2
2--0.22 Å20 Å2
3---3.76 Å2
Refinement stepCycle: 1 / Resolution: 2.37→86.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10709 0 1 35 10745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911019
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210335
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.95314908
X-RAY DIFFRACTIONr_angle_other_deg0.881323803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53151325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93823.952544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.614151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2321570
X-RAY DIFFRACTIONr_chiral_restr0.0770.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022623
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_it3.4824.9425342
X-RAY DIFFRACTIONr_mcbond_other3.4814.9425341
X-RAY DIFFRACTIONr_mcangle_it5.3857.4046652
X-RAY DIFFRACTIONr_mcangle_other5.3857.4046653
X-RAY DIFFRACTIONr_scbond_it3.5125.3195677
X-RAY DIFFRACTIONr_scbond_other3.5125.3195678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6367.8328256
X-RAY DIFFRACTIONr_long_range_B_refined8.41339.6412208
X-RAY DIFFRACTIONr_long_range_B_other8.41339.64212207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 41060 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.373→2.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 196 -
Rwork0.351 3850 -
obs--98.85 %

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