[English] 日本語
Yorodumi
- PDB-5o3x: Structural characterization of the fast and promiscuous macrocycl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o3x
TitleStructural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1
ComponentsPeptide cyclase 1
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
CACODYLATE ION / Prolyl endopeptidase
Similarity search - Component
Biological speciesVaccaria hispanica (cowherb)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide cyclase 1
B: Peptide cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2734
Polymers164,9992
Non-polymers2742
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein is a monomer according to size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)275.580, 60.850, 88.040
Angle α, β, γ (deg.)90.00, 92.65, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 8 - 724 / Label seq-ID: 8 - 724

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Peptide cyclase 1


Mass: 82499.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (cowherb) / Gene: Pcy1 / Plasmid: pJ414 / Details (production host): from DNA 2.0 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4P353
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 12.2 mg/mL PCY1 in 33% (w/v) PEG 2000, 113.75 mM Mg formate and 0.1 M Na cacodylate pH 7.0. For cryo protection 10% (v/v) glycerol were added to reservoir solution.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→87.95 Å / Num. obs: 44824 / % possible obs: 98.3 % / Redundancy: 3.3 % / Net I/σ(I): 11.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFS

1qfs


Resolution: 2.55→87.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 34.652 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26303 2362 5 %RANDOM
Rwork0.2165 ---
obs0.21882 44824 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 62.094 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å20 Å2-0.88 Å2
2--2.07 Å20 Å2
3---1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.55→87.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11414 0 10 139 11563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911721
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210645
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.95315876
X-RAY DIFFRACTIONr_angle_other_deg0.912324728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44451417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87723.969587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.835151972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8181576
X-RAY DIFFRACTIONr_chiral_restr0.0750.21679
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022503
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_it0.8062.9095677
X-RAY DIFFRACTIONr_mcbond_other0.8062.9095676
X-RAY DIFFRACTIONr_mcangle_it1.3954.3627088
X-RAY DIFFRACTIONr_mcangle_other1.3954.3627089
X-RAY DIFFRACTIONr_scbond_it0.6812.9766044
X-RAY DIFFRACTIONr_scbond_other0.6812.9776045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1664.4438788
X-RAY DIFFRACTIONr_long_range_B_refined4.15233.06112502
X-RAY DIFFRACTIONr_long_range_B_other4.14833.05112500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 45458 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 162 -
Rwork0.325 3310 -
obs--99.06 %
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)
12.38261.101-0.68583.4742-1.10952.6338-0.1140.1127-0.1121-0.30450.20270.5390.4134-0.953-0.08870.1703-0.15590.04590.7969-0.04340.3567289.895.6354.546
27.9269-1.9761.45132.9731-1.85713.6709-0.22350.38540.42420.05180.1147-0.0413-0.0279-0.0520.10880.1284-0.01920.10520.13150.00570.1918324.32319.664-3.033
32.85330.3322-0.0212.4852-0.31783.9912-0.1094-0.1763-0.0514-0.17310.03570.19120.5086-0.21390.07370.1865-0.00070.16350.13160.00210.2651326.933-1.4855.453
43.3719-0.53310.06952.1724-0.90452.976-0.0838-0.3530.3280.0153-0.0832-0.0708-0.14740.04450.1670.03810.0270.04030.3771-0.12250.2066330.72315.41720.871
52.7619-0.79670.1524.71461.0231.4772-0.1044-0.19030.8182-0.18160.0769-0.1072-0.4477-0.36420.02750.23050.18070.06030.558-0.23020.4683304.9428.48320.605
62.3667-0.08620.24811.5672-0.4092.7906-0.0728-0.32890.12-0.08840.12330.21040.2635-0.8578-0.05040.1087-0.020.09560.7386-0.08060.2547296.93812.79215.648
74.34270.12470.50241.0923-0.38871.25130.2152-0.2919-0.2470.1273-0.14110.124-0.2203-0.2568-0.07420.2584-0.00050.1380.3303-0.09120.1498302.79738.35-18.716
82.7546-0.33391.16762.7721-0.43135.0209-0.08240.10470.15330.25220.11140.1904-0.2069-0.3172-0.0290.1032-0.00920.14360.1658-0.03330.2634325.90451.519-25.051
92.98230.44540.57143.141-0.30432.6905-0.12820.80850.0546-0.09610.0915-0.0516-0.24110.41930.03670.1056-0.03040.10750.6458-0.04330.1824327.84341.69-44.583
109.37144.3425-2.1143.7888-2.58372.51980.03450.0259-0.67940.16320.0132-0.04380.25970.1544-0.04770.30090.05520.11590.3486-0.1440.336323.80222.855-30.724
113.38240.4417-0.22462.4585-0.66093.32280.070.323-0.16370.0532-0.0040.048-0.1135-0.0912-0.06610.04830.01580.07130.4539-0.09650.1513297.70633.746-37.555
121.7655-0.37380.25282.2197-1.58413.85830.1322-0.33530.01010.2449-0.0749-0.0404-0.4943-0.2769-0.05730.16530.0050.12790.4137-0.08910.2254288.79137.452-24.277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 73
2X-RAY DIFFRACTION2A74 - 134
3X-RAY DIFFRACTION3A135 - 272
4X-RAY DIFFRACTION4A273 - 434
5X-RAY DIFFRACTION5A435 - 490
6X-RAY DIFFRACTION6A491 - 724
7X-RAY DIFFRACTION7B5 - 124
8X-RAY DIFFRACTION8B125 - 272
9X-RAY DIFFRACTION9B273 - 382
10X-RAY DIFFRACTION10B383 - 440
11X-RAY DIFFRACTION11B441 - 625
12X-RAY DIFFRACTION12B626 - 724

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more