[English] 日本語
Yorodumi
- PDB-2l0q: NMR Solution Structure of Vibrio harveyi Acyl Carrier Protein (ACP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l0q
TitleNMR Solution Structure of Vibrio harveyi Acyl Carrier Protein (ACP)
ComponentsAcyl carrier protein
KeywordsLIPID BINDING PROTEIN / ACYL CARRIER PROTEIN / FATTY ACID BIOSYNTHESIS / ACYL CHAIN BINDING
Function / homology
Function and homology information


acyl carrier activity / cytoplasm
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesVibrio harveyi 1DA3 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsChan, D.I. / Chu, B.C.H. / Lau, C.K.Y. / Hunter, H.N. / Byers, D.M. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: NMR solution structure and biophysical characterization of Vibrio harveyi acyl carrier protein A75H: effects of divalent metal ions.
Authors: Chan, D.I. / Chu, B.C. / Lau, C.K. / Hunter, H.N. / Byers, D.M. / Vogel, H.J.
History
DepositionJul 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)8,8531
Polymers8,8531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Acyl carrier protein / ACP


Mass: 8852.664 Da / Num. of mol.: 1 / Mutation: A75H
Source method: isolated from a genetically manipulated source
Details: Holo-ACP present for structure determination, however phosphopantetheine coordinates not determined
Source: (gene. exp.) Vibrio harveyi 1DA3 (bacteria) / Gene: acpP, VME_27770 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0XCG4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Holo-Acyl Carrier Protein of V. harveyi; coordinates of phosphopantetheine group not calculated
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1212D 1H-1H NOESY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1512D 1H-1H TOCSY
1612D DQF-COSY
1712D DQF-COSY
1822D 1H-15N HSQC
1923D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM ACP, 0.1-0.5 mM DSS, 10 mM [U-2H] DTT, 10 mM potassium phosphate, 1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] ACP, 0.1-0.5 mM DSS, 10 mM [U-2H] DTT, 10 mM potassium phosphate, 1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1 mMACP-11
mMDSS-20.1-0.51
10 mMDTT-3[U-2H]1
10 mMpotassium phosphate-41
1 %sodium azide-51
1 mMACP-6[U-100% 15N]2
mMDSS-70.1-0.52
10 mMDTT-8[U-2H]2
10 mMpotassium phosphate-92
1 %sodium azide-102
Sample conditionsIonic strength: 0 / pH: 5.7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
XwinNMR3.0, 3.5Bruker Biospincollection
NMRDraw5.0 Rev 2009.103.20.08Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2009.015.15.35Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2.01Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2.01Johnson, One Moon Scientificdata analysis
NMRView5.2.2.01Johnson, One Moon Scientificpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1553 / NOE long range total count: 367 / NOE medium range total count: 405 / Hydrogen bond constraints total count: 56
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / 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