[English] 日本語
Yorodumi
- PDB-7mmy: Racemic structure of the cyclic plant peptide PDP-23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mmy
TitleRacemic structure of the cyclic plant peptide PDP-23
ComponentsPDP-23
KeywordsPLANT PROTEIN / PDP / head-to-tail cyclic / homodimer / racemic crystallography
Biological speciesZinnia elegans (garden zinnia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.464 Å
AuthorsVadlamani, G. / Bond, C.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130100890 Australia
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Solution NMR and racemic crystallography provide insights into a novel structural class of cyclic plant peptides.
Authors: Payne, C.D. / Vadlamani, G. / Hajiaghaalipour, F. / Muhammad, T. / Fisher, M.F. / Andersson, H.S. / Goransson, U. / Clark, R.J. / Bond, C.S. / Mylne, J.S. / Rosengren, K.J.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PDP-23
B: PDP-23


Theoretical massNumber of molelcules
Total (without water)6,2712
Polymers6,2712
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.527, 49.008, 29.402
Angle α, β, γ (deg.)90.000, 92.284, 90.000
Int Tables number14
Space group name H-MP121/n1

-
Components

#1: Protein/peptide PDP-23


Mass: 3135.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Zinnia elegans (garden zinnia)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.58 Å3/Da / Density % sol: 22.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were obtained from a racemic mix of 7mg/ml each of L- and D-peptide in 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% PEG monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.46→49.01 Å / Num. obs: 13346 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 515 / CC1/2: 0.833 / % possible all: 80.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L51

7l51


Resolution: 1.464→25.198 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.514 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2763 619 4.747 %
Rwork0.1881 12422 -
all0.192 --
obs-13041 98.691 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.907 Å2
Baniso -1Baniso -2Baniso -3
1--1.867 Å2-0 Å2-0.719 Å2
2---2.209 Å2-0 Å2
3---4.12 Å2
Refinement stepCycle: LAST / Resolution: 1.464→25.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms438 0 0 45 483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.012513
X-RAY DIFFRACTIONr_bond_other_d0.0010.017366
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.62715
X-RAY DIFFRACTIONr_angle_other_deg1.6641.554869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.137564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3622.524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2991549
X-RAY DIFFRACTIONr_chiral_restr0.1110.257
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02610
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02126
X-RAY DIFFRACTIONr_nbd_refined0.2210.294
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.2314
X-RAY DIFFRACTIONr_nbtor_refined0.20.2221
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.228
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.234
X-RAY DIFFRACTIONr_nbd_other0.2830.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.212
X-RAY DIFFRACTIONr_mcbond_it3.2631.894247
X-RAY DIFFRACTIONr_mcbond_other3.2511.894246
X-RAY DIFFRACTIONr_mcangle_it3.8582.873314
X-RAY DIFFRACTIONr_mcangle_other3.8542.872315
X-RAY DIFFRACTIONr_scbond_it5.1082.45266
X-RAY DIFFRACTIONr_scbond_other4.9992.443264
X-RAY DIFFRACTIONr_scangle_it5.8113.513400
X-RAY DIFFRACTIONr_scangle_other5.6693.508400
X-RAY DIFFRACTIONr_lrange_it5.12923.982551
X-RAY DIFFRACTIONr_lrange_other5.14523.674547
X-RAY DIFFRACTIONr_rigid_bond_restr8.9173879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.464-1.5020.355440.3027920.3059580.9490.95287.26510.277
1.502-1.5430.358490.2719040.2759580.9030.96699.47810.253
1.543-1.5880.292480.2748570.2759090.9480.96499.560.253
1.588-1.6360.333580.2588710.2629350.9210.9699.35830.236
1.636-1.690.289500.2517890.2538400.8950.95799.8810.232
1.69-1.7490.396390.2278090.2338510.9480.96699.64750.211
1.749-1.8140.305230.27890.2028140.9380.9899.75430.188
1.814-1.8880.246170.1827580.1837760.9680.98899.87110.175
1.888-1.9720.332340.1787310.1857660.9440.98599.86950.173
1.972-2.0670.289440.1926630.1987080.9350.97899.85880.194
2.067-2.1780.262300.1776460.1816770.9410.9899.85230.182
2.178-2.3090.197150.1726340.1736500.9690.98299.84620.182
2.309-2.4670.319310.1685750.1756110.960.98399.18170.186
2.467-2.6630.316160.1935480.1955650.9460.97899.8230.215
2.663-2.9140.27250.1794900.1835170.9530.97899.61320.203
2.914-3.2520.271340.1614250.1694640.9640.98498.92240.197
3.252-3.7450.215260.163950.1634240.9760.98599.29240.209
3.745-4.5610.29790.1393410.1423510.9750.9999.71510.191
4.561-6.3470.217190.1792550.1822760.9740.98499.27540.247
6.347-25.1980.28380.2331500.2351600.9660.96498.750.294

+
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