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- PDB-6ewt: Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12B-NDD -

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Basic information

Entry
Database: PDB / ID: 6ewt
TitleSolution Structure of Rhabdopeptide NRPS Docking Domain Kj12B-NDD
ComponentsNRPS Kj12B-NDD
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


organic substance biosynthetic process / 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 / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily ...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 / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NRPS Kj12B-NDD


Theoretical massNumber of molelcules
Total (without water)7,2451
Polymers7,2451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4670 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 Kj12B-NDD


Mass: 7245.112 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: A0A173DW12

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D H(CCO)NH
151isotropic13D C(CO)NH
1121isotropic13D HBHA(CO)NH
1111isotropic23D (H)CCH-TOCSY
1101isotropic23D (H)CCH-TOCSY
192isotropic12D 1H-15N HSQC
182isotropic13D 1H-15N NOESY-HSQC
171isotropic13D 1H-13C NOESY
161isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution2200 uM [U-15N] Kj12BCDD, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKj12BCDD[U-13C; U-15N]1
200 uMKj12BCDD[U-15N]2
Sample conditionsIonic strength: 100 mM / Label: NMR-buffer / pH: 6.5 / Pressure: AMBIENT bar / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE6002WW

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Processing

NMR software
NameVersionDeveloperClassification
OPALp3.97Guenthertrefinement
CARA3.97Keller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospinprocessing
CANDIDHerrmann, Guntert and Wuthrichpeak picking
CYANA3.97Guentert Peterstructure calculation
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

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