[English] 日本語
Yorodumi
- PDB-4ca3: SOLUTION STRUCTURE OF STREPTOMYCES VIRGINIAE VIRA ACP5B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ca3
TitleSOLUTION STRUCTURE OF STREPTOMYCES VIRGINIAE VIRA ACP5B
ComponentsHYBRID POLYKETIDE SYNTHASE-NON RIBOSOMAL PEPTIDE SYNTHETASE
KeywordsRIBOSOMAL PROTEIN / ACYL CARRIER PROTEIN / POLYKETIDE SYNTHASE
Function / homology
Function and homology information


toxin biosynthetic process / amide biosynthetic process / organic cyclic compound biosynthetic process / organonitrogen compound biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / ACP-like / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain ...: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / ACP-like / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / 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 / Phosphopantetheine attachment site. / Thiolase-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hybrid polyketide synthase-non ribosomal peptide synthetase
Similarity search - Component
Biological speciesSTREPTOMYCES VIRGINIAE (bacteria)
MethodSOLUTION NMR / CYANA
AuthorsDavison, J. / Dorival, J. / Rabeharindranto, M.H. / Chagot, B. / Gruez, A. / Weissman, K.J.
CitationJournal: Chem.Sci. / Year: 2014
Title: Insights Into the Function of Trans-Acyl Transferase Polyketide Synthases from the Saxs Structure of a Complete Module.
Authors: Davison, J. / Dorival, J. / Rabeharindranto, M.H. / Mazon, H. / Chagot, B. / Gruez, A. / Weissman, K.J.
History
DepositionOct 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_nmr_software
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYBRID POLYKETIDE SYNTHASE-NON RIBOSOMAL PEPTIDE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)9,2171
Polymers9,2171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein HYBRID POLYKETIDE SYNTHASE-NON RIBOSOMAL PEPTIDE SYNTHETASE / ACYL CARRIER PROTEIN 5B


Mass: 9217.263 Da / Num. of mol.: 1 / Fragment: VIRA, RESIDUES 6831-6914
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VIRGINIAE (bacteria) / Plasmid: PBG102 (PET27 DERIVATIVE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4PHN0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D NOESYS
121HN(CA)CB
131CBCA(CO)NH
141HCCHTOCSY
151HCCHCOSY
161HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C,15N ACP5B

-
Sample preparation

DetailsContents: 100 MM PHOSPHATE BUFFER, 1MM EDTA
Sample conditionsIonic strength: 100 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Amber11D.A. CASE,T.A.DARDEN,T.E.CHEATHAM,III, C.L.SIMMERLING,J.WANG,R.E.DUKE,R.LUO,R.C.WALKER, W.ZHANG,K.M.MERZ,B.ROBERTS,S.HAYIK,A.ROITBERG, G.SEABRA,J.SWAILS,A.W.GOETZ,I.KOLOSSVARY,K.F. WONG,F.PAESANI,J.VANICEK,R.M.WOLF,J.LIU,X.WU, S.R.BROZELL,T.STEINBRECHER,H.GOHLKE,Q.CAI,X.YE, J.WANG,M.-J.HSIEH,G.CUI,D.R.ROE,D.H.MATHEWS, M.G.SEETIN,R.SALOMON-FERRER,C.SAGUI,V.BABIN,T. LUCHKO,S.GUSAROV,A.KOVALENKO,refinement
Sparkystructure solution
RefinementMethod: CYANA / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / 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