[English] 日本語
Yorodumi
- PDB-2liw: NMR structure of HMG-ACPI domain from CurA module from Lyngbya ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2liw
TitleNMR structure of HMG-ACPI domain from CurA module from Lyngbya majuscula
ComponentsCurA
KeywordsTRANSFERASE / PKS
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
CurL-like, PKS C-terminal / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / ACP-like / PKS_PP_betabranch / Malonyl-CoA ACP transacylase, ACP-binding / : / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase / Acyl transferase domain ...CurL-like, PKS C-terminal / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / ACP-like / PKS_PP_betabranch / Malonyl-CoA ACP transacylase, ACP-binding / : / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Acetyltransferase (GNAT) family / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-HYDROXY-3-METHYL-GLUTARIC ACID / 4'-PHOSPHOPANTETHEINE / CurA
Similarity search - Component
Biological speciesLyngbya majuscula (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBusche, A.E. / Gottstein, D. / Hein, C. / Ripin, N. / Pader, I. / Tufar, P. / Eisman, E.B. / Gu, L. / Walsh, C.T. / Loehr, F. ...Busche, A.E. / Gottstein, D. / Hein, C. / Ripin, N. / Pader, I. / Tufar, P. / Eisman, E.B. / Gu, L. / Walsh, C.T. / Loehr, F. / Sherman, D.H. / Guntert, P. / Dotsch, V.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Characterization of Molecular Interactions between ACP and Halogenase Domains in the Curacin A Polyketide Synthase.
Authors: Busche, A. / Gottstein, D. / Hein, C. / Ripin, N. / Pader, I. / Tufar, P. / Eisman, E.B. / Gu, L. / Walsh, C.T. / Sherman, D.H. / Lohr, F. / Guntert, P. / Dotsch, V.
History
DepositionSep 1, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5303
Polymers11,0091
Non-polymers5202
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 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein CurA


Mass: 11009.310 Da / Num. of mol.: 1 / Fragment: UNP residues 1946-2034
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6DNF2
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-MAH / 3-HYDROXY-3-METHYL-GLUTARIC ACID


Mass: 162.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O5 / Comment: alkaloid*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1243D HN(CA)CB
1343D HNCO
1443D HN(CA)CO
1543D H(CCO)NH-TOCSY
1643D (H)C(CCO)NH-TOCSY
1723D 1H-13C NOESY
1813D 1H-15N NOESY
194(H)CB(CGCC- TOCSY)Har
1103F1-13C/15N-filtered, F3-13C-seperated NOESY-HSQC
11132D F1/F2-13C/15N double-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 15N] Holo ACPI, 5 % D2O, 0.15 mM DSS, 50 mM Glutamate, 50 mM Arginine, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-13C] Holo ACPI, 5 % D2O, 0.15 mM DSS, 50 mM Arginine, 50 mM Glutamate, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-13C] and [U-N15] HMG ACPI, 0.15 mM D2O, 5 % DSS, 50 mM NaCL, 25 mM NaPi, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-15N] and (13C) Holo ACPI, 5 % D2O, 0.15 mM DSS, 50 mM Glutamate, 50 mM Arginine, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHolo ACPI-1[U-98% 15N]1
5 %D2O-21
0.15 mMDSS-31
50 mMGlutamate-41
50 mMArginine-51
1 mMHolo ACPI-6[U-13C]2
5 %D2O-72
0.15 mMDSS-82
50 mMArginine-92
50 mMGlutamate-102
1 mMHMG ACPI-11[U-13C] and [U-N15]3
0.15 mMD2O-123
5 %DSS-133
50 mMNaCL-143
25 mMNaPi-153
1 mMHolo ACPI-16[U-15N] and (13C)4
5 %D2O-174
0.15 mMDSS-184
50 mMGlutamate-194
50 mMArginine-204
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 291 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance6002
Bruker AvanceBrukerAvance8003
Bruker AvanceBrukerAvance9004
Bruker AvanceBrukerAvance9505

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1 and 3.0Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1 and 3.0Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / 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