[English] 日本語
Yorodumi
- PDB-8cuf: Synthetic epi-Novo29 (2R,3S), X-ray diffractometer structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cuf
TitleSynthetic epi-Novo29 (2R,3S), X-ray diffractometer structure
ComponentsSynthetic epi-Novo29 (2R,3S)
KeywordsANTIBIOTIC / macrocyclic peptide
Function / homologyACETATE ION / IODIDE ION
Function and homology information
Biological speciesEleftheria (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.68 Å
AuthorsKreutzer, A.G. / Li, X. / Krumberger, M. / Nowick, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Org.Chem. / Year: 2023
Title: Synthesis and Stereochemical Determination of the Peptide Antibiotic Novo29.
Authors: Krumberger, M. / Li, X. / Kreutzer, A.G. / Peoples, A.J. / Nitti, A.G. / Cunningham, A.M. / Jones, C.R. / Achorn, C. / Ling, L.L. / Hughes, D.E. / Nowick, J.S.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synthetic epi-Novo29 (2R,3S)
B: Synthetic epi-Novo29 (2R,3S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1555
Polymers1,8422
Non-polymers3133
Water32418
1
A: Synthetic epi-Novo29 (2R,3S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2344
Polymers9211
Non-polymers3133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synthetic epi-Novo29 (2R,3S)


  • defined by author
  • 921 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9211
Polymers9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)12.103, 31.555, 36.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Synthetic epi-Novo29 (2R,3S)


Mass: 921.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Eleftheria (bacteria)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 2.8 M sodium acetate trihydrate, pH 6.6

-
Data collection

DiffractionMean temperature: 123.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→24 Å / Num. obs: 2869 / % possible obs: 95.61 % / Redundancy: 13.1 % / CC1/2: 0.869 / Net I/σ(I): 36.1
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 111 / CC1/2: 0.822

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→24 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 11.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 289 10.07 %
Rwork0.1517 2580 -
obs0.1532 2869 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.92 Å2 / Biso mean: 10.8764 Å2 / Biso min: 1.21 Å2
Refinement stepCycle: final / Resolution: 1.68→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms128 0 7 18 153
Biso mean--10.61 19.07 -
Num. residues----18
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-2.110.19751300.16781168129883
2.11-240.15491590.144814121571100

+
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