[English] 日本語
Yorodumi
- PDB-8qpy: Solution NMR structure of the peptidyl carrier domain TomAPCP fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qpy
TitleSolution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase
ComponentsCarrier protein TomAPCP
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / Tomaymycin / PCP / phosphopantetheine / Donor
Biological speciesStreptomyces regensis (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics / molecular dynamics
AuthorsKaranth, M.N. / Kirkpatrick, J.P. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CA294/16-1 Germany
CitationJournal: Sci Adv / Year: 2024
Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain.
Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T.
History
DepositionOct 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carrier protein TomAPCP


Theoretical massNumber of molelcules
Total (without water)10,3801
Polymers10,3801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #9closest to the average

-
Components

#1: Protein Carrier protein TomAPCP


Mass: 10380.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the ...Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the fifth residue has residue-number '1'. A special modified residue SPP is designated for the serine residue covalently linked to a 4'-phosphopantetheine prosthetic group.
Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli BL21(DE3) (bacteria)
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D H(CCO)NH
171isotropic13D C(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D HBHA(CO)NH
1101isotropic13D 1H-15N NOESY
1111isotropic32D 1H-13C HSQC
1121isotropic12D hbcbcgcdhdgp
1131isotropic12D hbcbcgcdcehegp
1142isotropic22D 1H-13C HSQC
1152isotropic23D 1H-13C NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-13C; U-15N] APCP, 50 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT, 10 v/v [U-2H] D2O, 0.02 % w/v sodium azide, 90% H2O/10% D2OMain sample used for assignment and collection of distance restraints.13C15N_sample90% H2O/10% D2O
solution2500 uM [U-13C; U-15N] APCP, 50 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT, 0.02 w/v sodium azide, 100 % v/v [U-2H] D2O, 100% D2OAdditional sample (dissolved in D2O-based buffer) used for collection of distance restraints.13C15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMAPCP[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
10 v/vD2O[U-2H]1
0.02 % w/vsodium azidenatural abundance1
500 uMAPCP[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
0.02 w/vsodium azidenatural abundance2
100 % v/vD2O[U-2H]2
Sample conditionsIonic strength: 265 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE III HDBrukerAVANCE III HD8503

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipe10.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4CCPNpeak picking
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing7
torsion angle dynamics8
molecular dynamics9
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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