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- PDB-7b2f: Solution structure of the Pax NRPS docking domain PaxB NDD -

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Basic information

Entry
Database: PDB / ID: 7b2f
TitleSolution structure of the Pax NRPS docking domain PaxB NDD
ComponentsPeptide synthetase XpsB (Modular protein)
KeywordsPROTEIN BINDING / PROTEIN
Biological speciesXenorhabdus cabanillasii JM26 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsWatzel, J. / Sarawi, S. / Duchardt-Ferner, E. / Bode, H.B. / Woehnert, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS.
Authors: Watzel, J. / Duchardt-Ferner, E. / Sarawi, S. / Bode, H.B. / Wohnert, J.
History
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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
Revision 1.3Jun 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: Peptide synthetase XpsB (Modular protein)


Theoretical massNumber of molelcules
Total (without water)3,6161
Polymers3,6161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3760 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 Peptide synthetase XpsB (Modular protein)


Mass: 3616.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus cabanillasii JM26 (bacteria)
Gene: XCR1_1150011 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: (2,3-dihydroxybenzoyl)adenylate synthase, ornithine racemase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic13D HNCO
172isotropic33D HN(CA)CB
162isotropic13D HBHA(CO)NH
1152isotropic23D C(CO)NH
1142isotropic23D H(CCO)NH
131isotropic23D 1H-15N NOESY
182isotropic22D 1H-13C HSQC aliphatic
142isotropic23D 1H-13C NOESY aliphatic
153isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution2300 uM [U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O15N,13C_sample95% H2O/5% D2O
solution3300 uM [U-10% 13C; U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O15N,13C_stereo_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMPaxB NDD[U-15N]1
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
5 %D2O[U-2H]1
100 uMDSSnatural abundance1
300 uMPaxB NDD[U-15N]2
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
5 %D2O[U-2H]2
100 uMDSSnatural abundance2
300 uMPaxB NDD[U-10% 13C; U-15N]3
50 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
5 %D2O[U-2H]3
100 uMDSSnatural abundance3
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 AVANCE III HDBrukerAVANCE III HD8001
Bruker AVANCE IIBrukerAVANCE II6002
Bruker AVANCE III HDBrukerAVANCE III HD7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospindata analysis
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
OPALpKoradi, Billeter and Guntertrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics4
molecular dynamics5
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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