[English] 日本語
Yorodumi
- PDB-8a7z: NMR structure of holo-acp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a7z
TitleNMR structure of holo-acp
ComponentsHybrid polyketide synthase-non ribosomal peptide synthetase
KeywordsTRANSFERASE / Acyl carrier protein
Function / homology
Function and homology information


toxin biosynthetic process / amide biosynthetic process / : / DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process ...toxin biosynthetic process / amide biosynthetic process / : / DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / Condensation domain ...: / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Hybrid polyketide synthase-non ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCollin, S. / Weissman, K.J. / Chagot, B. / Gruez, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2023
Title: Decrypting the programming of beta-methylation in virginiamycin M biosynthesis.
Authors: Collin, S. / Cox, R.J. / Paris, C. / Jacob, C. / Chagot, B. / Weissman, K.J. / Gruez, A.
History
DepositionJun 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hybrid polyketide synthase-non ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2412
Polymers8,8831
Non-polymers3581
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Hybrid polyketide synthase-non ribosomal peptide synthetase


Mass: 8882.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virA / Plasmid: pBG102 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A4PHN0
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
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 H(CCO)NH
141isotropic13D C(CO)NH
151isotropic13D (H)CCH-TOCSY
161isotropic13D CCH-TOCSY
171isotropic12D (HB)CB(CGCD)HD
181isotropic12D (HB)CB(CGCDCE)HE
191isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aromatic
1101isotropic12D 1H-15N
1131isotropic12D TOCSY H(C12-N14)
1141isotropic12D NOESY H(C12-N14)
1151isotropic12D NOESY H-H(C12-N14)

-
Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] acp5a-holo, 100 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMacp5a-holo[U-13C; U-15N]1
100 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
Sample conditionsDetails: 100 mM NaP / Ionic strength: 100 mM / Label: condition_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY1.47Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee et al. 2015chemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospincollection
NMRFAM-SPARKY1.47Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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