[English] 日本語
Yorodumi
- PDB-6ews: Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12A-NDD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ews
TitleSolution Structure of Rhabdopeptide NRPS Docking Domain Kj12A-NDD
ComponentsNRPS Kj12A-NDD
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


phosphopantetheine binding / catalytic activity
Similarity search - Function
TubC, N-terminal docking domain / TubC N-terminal docking domain / AMP-binding / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site ...TubC, N-terminal docking domain / TubC N-terminal docking domain / AMP-binding / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / 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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Nonribosomal peptide synthetase StoA
Similarity search - Component
Biological speciesXenorhabdus stockiae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHacker, C. / Cai, X. / Kegler, C. / Zhao, L. / Weickhmann, A.K. / Bode, H.B. / Woehnert, J.
CitationJournal: Nat Commun / Year: 2018
Title: Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS.
Authors: Hacker, C. / Cai, X. / Kegler, C. / Zhao, L. / Weickhmann, A.K. / Wurm, J.P. / Bode, H.B. / Wohnert, J.
History
DepositionNov 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NRPS Kj12A-NDD


Theoretical massNumber of molelcules
Total (without water)7,4961
Polymers7,4961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5000 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

-
Components

#1: Protein NRPS Kj12A-NDD


Mass: 7496.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus stockiae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A173DW33

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic22D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D (H)CCH-TOCSY
1101isotropic13D (H)CCH-TOCSY
192isotropic23D 1H-15N NOESY
181isotropic42D 1H-13C HSQC aliphatic
171isotropic43D 1H-13C NOESY aliphatic
161isotropic32D 1H-13C HSQC aromatic
1111isotropic33D 1H-13C NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution2500 uM [U-15N] Kj12A NDD, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKj12A NDD[U-13C; U-15N]1
500 uMKj12A NDD[U-15N]2
Sample conditionsIonic strength: 100 mM / Label: NMR_sample / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE9504
Bruker AVANCEBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guentertstructure calculation
TopSpin3.97Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CANDIDHerrmann, Guntert and Wuthrichpeak picking
OPALprefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
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