[English] 日本語
Yorodumi
- PDB-2ju1: Solution structure of acyl carrier protein domain from module 2 o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ju1
TitleSolution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS)
ComponentsErythronolide synthase
KeywordsTRANSFERASE / carrier protein domain / modular polyketide synthase / alpha-helical bundle / Acyltransferase / Antibiotic biosynthesis / Multifunctional enzyme / NADP / Phosphopantetheine
Function / homology
Function and homology information


erythronolide synthase activity / 6-deoxyerythronolide-B synthase / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
CurL-like, PKS C-terminal / ACP-like / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase ...CurL-like, PKS C-terminal / ACP-like / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / 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 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythronolide synthase EryA1
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsresidues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493)
AuthorsAlekseyev, V.Y. / Liu, C.W. / Puglisi, J.D. / Khosla, C.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase.
Authors: Alekseyev, V.Y. / Liu, C.W. / Cane, D.E. / Puglisi, J.D. / Khosla, C.
History
DepositionAug 12, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Erythronolide synthase


Theoretical massNumber of molelcules
Total (without water)10,1611
Polymers10,1611
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)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Erythronolide synthase / ORF 1 / 6-deoxyerythronolide B synthase I / DEBS 1


Mass: 10160.617 Da / Num. of mol.: 1 / Fragment: acyl carrier protein domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria)
Description: stop codon at the C-terminus, before the C-terminal His-tag present in the plasmid
Gene: eryA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03131, 6-deoxyerythronolide-B synthase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: residues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C/15N NOESY
1313D (H)CCH-TOCSY
1413D HNHA
1512D 1H-15N HSQC
1613D HN(CA)CB
1713D C(CO)NH

-
Sample preparation

DetailsContents: 0.8-1 mM [U-13C; U-15N] acyl carrier protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: acyl carrier protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 30 / pH: 5.5 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P. et al.structure solution
DYANA1.5Guntert, P. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The standard simulated annealing protocol included as part of DYANA software was used with 4000 steps per structure.
NMR constraintsNOE constraints total: 1791 / NOE intraresidue total count: 327 / NOE long range total count: 438 / NOE medium range total count: 540 / NOE sequential total count: 486 / Protein phi angle constraints total count: 50
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30 / Maximum upper distance constraint violation: 0.4 Å

+
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