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Basic information

Entry
Database: PDB / ID: 5o3v
TitleStructural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin B1
Components
  • Peptide cyclase 1
  • Putative presegetalin B1
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 / 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
Putative presegetalin B1 / Prolyl endopeptidase
Similarity search - Component
Biological speciesVaccaria hispanica (bladder-soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLudewig, H. / Czekster, C.M. / Bent, A.F. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council339367 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 1.3May 8, 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_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
D: Putative presegetalin B1
C: Putative presegetalin B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,95910
Polymers171,5264
Non-polymers4336
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.860, 65.200, 140.170
Angle α, β, γ (deg.)90.00, 95.91, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA4 - 7244 - 724
21SERSERASPASPBB4 - 7244 - 724
12VALVALPROPRODC2 - 1715 - 30
22VALVALPROPROCD2 - 1715 - 30

NCS ensembles :
ID
1
2

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Components

#1: Protein Peptide cyclase 1


Mass: 82483.266 Da / Num. of mol.: 2 / 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 Putative presegetalin B1


Mass: 3279.739 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6LNL6
#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PCY1-S562A complex with PresegB1 was crystallized at 13.3 mg/mL with 0.163 mM PresegB1 in 34.5% (w/v) PEG 3350 and 70 mM Mg sulfate. For cryo protection 5 % (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: 2.17→47.62 Å / Num. obs: 80090 / % possible obs: 99.5 % / Redundancy: 3.4 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→47.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.156 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24803 4273 5.1 %RANDOM
Rwork0.21572 ---
obs0.21732 80090 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 44.405 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20.38 Å2
2---0.2 Å20 Å2
3----3.01 Å2
Refinement stepCycle: 1 / Resolution: 2.17→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11692 0 22 257 11971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912068
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210943
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.95216364
X-RAY DIFFRACTIONr_angle_other_deg0.919325428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18251471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33723.946598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.778152017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9291576
X-RAY DIFFRACTIONr_chiral_restr0.0770.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022581
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_it1.31.1455848
X-RAY DIFFRACTIONr_mcbond_other1.2961.1445847
X-RAY DIFFRACTIONr_mcangle_it2.1151.7077301
X-RAY DIFFRACTIONr_mcangle_other2.1161.7087302
X-RAY DIFFRACTIONr_scbond_it1.8131.3116218
X-RAY DIFFRACTIONr_scbond_other1.7791.2996202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8581.899029
X-RAY DIFFRACTIONr_long_range_B_refined5.25213.02212390
X-RAY DIFFRACTIONr_long_range_B_other5.25213.02412391
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)
11A455600.05
12B455600.05
21D4060.1
22C4060.1
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 328 -
Rwork0.33 5874 -
obs--99.77 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.87360.84590.67533.36630.46682.74220.14130.4848-0.4433-0.51360.03340.08990.40930.2947-0.17470.18370.1012-0.12150.3303-0.1410.4363-7.267-12.244287.494
21.9665-0.17850.25941.7477-2.58025.0829-0.1939-0.2463-0.10860.32640.31010.05-0.5741-0.186-0.11620.12320.087-0.01140.16010.00180.3241-2.153.123322.615
32.0953-1.04190.40880.9668-0.3071.7547-0.1036-0.4284-0.7588-0.02520.28370.38030.1117-0.3129-0.18010.03720.0157-0.01180.26710.21780.6863-12.896-18.113324.77
42.4672-0.60630.79071.9231-0.68112.0742-0.1225-0.7423-0.5540.10250.36170.2546-0.1342-0.5262-0.23920.04240.14750.08880.58180.26640.5834-31.902-4.958329.971
53.19022.6325-2.47942.7932-3.25554.34410.0659-0.70050.06770.3348-0.19560.0249-0.5857-0.05750.12970.51780.38180.02030.71490.01560.4738-19.27211.917328.717
61.8295-0.74030.65550.9781-0.15851.5521-0.05630.0298-0.1750.03070.14830.2253-0.1108-0.2456-0.09190.01040.019-0.01490.23410.03010.3822-22.4014.448300.746
71.6789-0.31861.07491.1227-0.8812.30850.12480.4505-0.2444-0.10220.00980.10240.10630.2396-0.13450.01570.0247-0.03220.2937-0.05440.4071-9.354-0.407291.865
82.92830.3565-0.82783.3588-0.17873.78590.14130.62310.5247-0.57460.0424-0.0755-0.5668-0.1789-0.18370.19990.03670.01560.42950.18330.437521.82534.983290.34
91.4934-0.5266-1.10341.72371.56132.5946-0.0763-0.0440.29850.15020.1195-0.06180.1869-0.1731-0.04320.05050.0339-0.09920.2211-0.03830.458112.4130.231325.411
102.9873-0.5602-1.01944.1585-3.46677.5345-0.0273-0.1120.5432-0.17170.3602-0.21340.07880.424-0.33280.0283-0.015-0.08930.3731-0.21650.631730.96641.511330.003
112.1356-0.3048-0.50762.01921.76133.2049-0.1466-0.68970.36430.21360.3698-0.17240.49540.7886-0.22320.1410.2395-0.18040.6538-0.24320.488836.54427.807336.686
122.3718-0.3109-1.04651.72220.84382.8976-0.3568-0.2255-0.21560.35220.3349-0.10290.97770.5540.02190.36270.2409-0.08090.2964-0.02260.395430.8949.927317.113
132.1048-0.6313-0.77441.85510.18082.98590.03730.10310.4956-0.1110.1982-0.2835-0.09590.6246-0.23550.0149-0.0227-0.02270.3444-0.03980.452736.85427.903302.865
141.68180.0077-0.67111.47650.35823.21340.00660.50010.1855-0.23010.0458-0.05480.0609-0.031-0.05240.05480.0001-0.05660.33160.03330.356423.85823.36295.346
1510.84844.91884.036210.61291.92351.5605-0.2213-0.54630.4921-0.1624-0.1910.9907-0.0734-0.34050.41230.31340.00150.03420.5236-0.09540.5059-7.5194.003315.289
161.38692.9431.227116.71017.3893.32560.3526-0.30640.54480.828-0.0833-0.5940.31190.1887-0.26930.3656-0.0830.02320.82770.03480.659617.48518.992318.004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 60
2X-RAY DIFFRACTION2A61 - 148
3X-RAY DIFFRACTION3A149 - 266
4X-RAY DIFFRACTION4A267 - 381
5X-RAY DIFFRACTION5A382 - 430
6X-RAY DIFFRACTION6A431 - 627
7X-RAY DIFFRACTION7A628 - 724
8X-RAY DIFFRACTION8B4 - 60
9X-RAY DIFFRACTION9B61 - 230
10X-RAY DIFFRACTION10B231 - 266
11X-RAY DIFFRACTION11B267 - 401
12X-RAY DIFFRACTION12B402 - 522
13X-RAY DIFFRACTION13B523 - 627
14X-RAY DIFFRACTION14B628 - 724
15X-RAY DIFFRACTION15C2 - 14
16X-RAY DIFFRACTION16D1 - 14

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