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- PDB-6trp: Solution Structure of Docking Domain Complex of Pax NRPS: PaxC ND... -

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Basic information

Entry
Database: PDB / ID: 6trp
TitleSolution Structure of Docking Domain Complex of Pax NRPS: PaxC NDD - PaxB CDD
ComponentsPeptide synthetase XpsB,Peptide synthetase XpsB
KeywordsPROTEIN BINDING / Protein / NRPS / Docking Domains / Communication-Mediating Domains
Function / homology
Function and homology information


ornithine racemase / (2,3-dihydroxybenzoyl)adenylate synthase / ornithine racemase activity / phenylalanine racemase (ATP-hydrolysing) / o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / phenylalanine racemase (ATP-hydrolyzing) activity / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / biosynthetic process / phosphopantetheine binding
Similarity search - Function
Thioesterase / Thioesterase domain / 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 ...Thioesterase / Thioesterase domain / 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 / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Peptide synthetase XpsB / Peptide synthetase XpsB
Similarity search - Component
Biological speciesXenorhabdus bovienii SS-2004 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsWatzel, J. / Hacker, C. / Duchardt-Ferner, E. / Bode, H.B. / Woehnert, J.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase fromXenorhabdus bovienii.
Authors: Watzel, J. / Hacker, C. / Duchardt-Ferner, E. / Bode, H.B. / Wohnert, J.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.field_strength
Revision 1.2Jun 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: Peptide synthetase XpsB,Peptide synthetase XpsB


Theoretical massNumber of molelcules
Total (without water)9,8421
Polymers9,8421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8260 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Peptide synthetase XpsB,Peptide synthetase XpsB


Mass: 9841.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus bovienii SS-2004 (bacteria)
Gene: XBJ1_2151, XBJ1_2152 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D3V3G2, UniProt: D3V3G3, (2,3-dihydroxybenzoyl)adenylate synthase, ornithine racemase, phenylalanine racemase (ATP-hydrolysing), o-succinylbenzoate-CoA ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC, 3D b-tr-HN(CA)CB, 3D b-tr-HNCO, 3D HC(C)H-TOCSY
121isotropic22D 1H-15N HSQC, 3D (H)CCH-TOCSY
132isotropic32D 1H-15N HSQC, 3D HBHA(CO)NH, 3D HN(CA)CO, 3D H(CCO)NH
143isotropic42D 1H-15N HSQC, 3D 1H-15N NOESY
152isotropic12D 1H-13C HSQC aliphatic, 3D 1H-13C NOESY aliphatic
162isotropic12D 1H-13C HSQC aromatic, 3D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1370 uM [U-99% 13C; U-99% 15N] PaxC NDD 12.5xGS Y-PaxB CDD, 90% H2O/10% D2O15N,13C_sample#190% H2O/10% D2O
solution21620 uM [U-99% 13C; U-99% 15N] PaxC NDD 12.5xGS Y-PaxB CDD, 90% H2O/10% D2O15N,13C_sample#290% H2O/10% D2O
solution3730 uM [U-99% 15N] PaxC NDD 12.5xGS Y-PaxB CDD, 90% H2O/10% D2O15N_sample#190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
370 uMPaxC NDD 12.5xGS Y-PaxB CDD[U-99% 13C; U-99% 15N]1
1620 uMPaxC NDD 12.5xGS Y-PaxB CDD[U-99% 13C; U-99% 15N]2
730 uMPaxC NDD 12.5xGS Y-PaxB CDD[U-99% 15N]3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: AMBIENT bar / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guentert, Peterrefinement
CARA1.8.4.2Keller, Rochus and Wuethrich, Kurtchemical shift assignment
TopSpin3.5Bruker Biospincollection
CcpNmr Analysis2.4.2CCPNdata analysis
UNIO10Herrmann, Thorsten, Guentert, Peter and Wuethrich, Kurtpeak picking
CYANAGuentert, Peter, Mumenthaler, Christian and Wuethrich, Kurtstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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