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- PDB-6ewu: Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-NDD -

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Basic information

Entry
Database: PDB / ID: 6ewu
TitleSolution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-NDD
ComponentsNRPS Kj12C-NDD
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity / cytoplasm
Similarity search - Function
TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Nonribosomal peptide synthetase StoC
Similarity search - Component
Biological speciesXenorhabdus stockiae (bacteria)
MethodSOLID-STATE NMR / Energy refinement, molecular dynamics simulation algorithm for biomolecules
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 1.1Aug 21, 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 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NRPS Kj12C-NDD


Theoretical massNumber of molelcules
Total (without water)7,3221
Polymers7,3221
Non-polymers00
Water00
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 area4680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein NRPS Kj12C-NDD


Mass: 7322.091 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: A0A173DW42

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY aliphatic
132isotropic13D 1H-13C NOESY aromatic
142isotropic83D HN(CA)CB
152isotropic83D HNCO
1202isotropic83D HN(CA)CO
1192isotropic13D HBHA(CO)NH
1182isotropic83D H(CCO)NH
1172isotropic83D (H)C(CCO)NH
1162isotropic103D (H)CCH-TOCSY
1152isotropic103D (H)CCH-TOCSY
1142isotropic12D 1H-13C HSQC aliphatic
1132isotropic12D 1H-13C HSQC aromatic
1121isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1200 uM [U-15N] Kj12CDD, 90% H2O/10% D2O15N90% H2O/10% D2O
solution2700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O13C,15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMKj12CDD[U-15N]1
700 uMKj12CDD[U-13C; U-15N]2
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE60010Wasserwerk
Bruker AVANCEBrukerAVANCE7009
Bruker AVANCEBrukerAVANCE8008
Bruker AVANCEBrukerAVANCE8007Wasserwerk
Bruker AVANCEBrukerAVANCE9506

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guentertstructure calculation
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
UNIO'10 (ATNOS/CANDID(3) Herrmann, T.; uentert, P.; Wuethrich, K. J. Mol. Biol. 2002, 319, 209-227. (4) Herrmann, T.; Guentert, P.; Wuethrich, K. J. Biomol. NMR 2002, 24, 171-189.peak picking
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: Energy refinement, molecular dynamics simulation algorithm for biomolecules
Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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