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- PDB-6ewv: Solution Structure of Docking Domain Complex of RXP NRPS: Kj12C N... -

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Basic information

Entry
Database: PDB / ID: 6ewv
TitleSolution Structure of Docking Domain Complex of RXP NRPS: Kj12C NDD - Kj12B CDD
ComponentsNRPS Kj12C-NDD, NRPS Kj12B-CDD
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN / Solution Structure / Rhabdopeptide / Docking Domains
Function / homology
Function and homology information


: / catalytic activity
Similarity search - Function
TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / TubC N-terminal docking domain / Methyltransferase domain 25 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site ...TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / TubC N-terminal docking domain / Methyltransferase domain 25 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Nonribosomal peptide synthetase StoB / Nonribosomal peptide synthetase StoC
Similarity search - Component
Biological speciesXenorhabdus stockiae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsHacker, C. / Cai, X. / Kegler, C. / Zhao, L. / Weickhmann, A.K. / Bode, H.B. / Woehnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
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
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NRPS Kj12C-NDD, NRPS Kj12B-CDD


Theoretical massNumber of molelcules
Total (without water)11,1071
Polymers11,1071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein NRPS Kj12C-NDD, NRPS Kj12B-CDD


Mass: 11107.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus stockiae (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A173DW42, UniProt: A0A173DW12

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
191isotropic22D 1H-15N b-tr-HSQC
122isotropic13D 1H-13C NOESY
1112isotropic12D 1H-13C HSQC aliphatic
1102isotropic12D 1H-13C HSQC aromatic
132isotropic63D (H)CCH-TOCSY
142isotropic53D (H)CCH-TOCSY
152isotropic53D HBHA(CO)NH
182isotropic23D b-tr-HNCO
172isotropic23D b-tr-HN(CA)CB
162isotropic23D b-tr-HN(CO)CA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1700 uM [U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution2850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMKJ12C Ndd 12xGS KJ12B Cdd[U-99% 15N]1
850 uMKJ12C Ndd 12xGS KJ12B Cdd[U-99% 13C; U-99% 15N]2
Sample conditionsDetails: 50 mM sodium phosphate buffer at pH 6.5 150 mM sodium chloride
Ionic strength: 150 mM / Label: NMR buffer / 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 AVANCEBrukerAVANCE8005
Bruker AVANCEBrukerAVANCE6006ww

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Processing

NMR software
NameVersionDeveloperClassification
OPALp3.97Guentert Peterrefinement
CARA1.8.4.2Keller, R. (2004) The Computer Aided Resonance Tutorial, CANTINA Verlag, Goldauchemical shift assignment
TopSpin3.5Bruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
UNIO10Herrmann, Thorsten, Guentert, Peter and Wuethrich, Kurtpeak picking
CYANA3.97Guentert Peterstructure calculation
RefinementMethod: molecular 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

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