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- PDB-5ttb: Solution structure of apo ArCP from yersiniabactin synthetase -

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Basic information

Entry
Database: PDB / ID: 5ttb
TitleSolution structure of apo ArCP from yersiniabactin synthetase
ComponentsSiderophore yersiniabactin
KeywordsLIGASE / apo carrier protein / nonribosomal peptide synthetase
Function / homology
Function and homology information


Condensation domain / Condensation domain / ACP-like / Chloramphenicol acetyltransferase-like domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. ...Condensation domain / Condensation domain / ACP-like / Chloramphenicol acetyltransferase-like domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Siderophore yersiniabactin
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsFrueh, D.P. / Goodrich, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104257 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication.
Authors: Goodrich, A.C. / Meyers, D.J. / Frueh, D.P.
History
DepositionNov 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.6May 15, 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: Siderophore yersiniabactin


Theoretical massNumber of molelcules
Total (without water)9,7711
Polymers9,7711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest CYANA target function
RepresentativeModel #1lowest energy structure

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Components

#1: Protein Siderophore yersiniabactin


Mass: 9771.064 Da / Num. of mol.: 1 / Fragment: residues 14-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: irp2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2UWU4

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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
122isotropic12D 1H-13C HSQC
233isotropic12D 1H-13C HSQC
141isotropic13D 1H-15N NOESY
253isotropic13D 1H-13C NOESY
162isotropic13D HNCO
172isotropic13D HNCA
182isotropic13D HN(CA)CB
192isotropic13D H(CCCO)NH
1102isotropic13D HN(CA)CO
2113isotropic12D (HB)CB(CGCD)HD
2123isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.25 mM [U-99% 15N] apo-ArCP, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.25 mM [U-99% 13C; U-99% 15N] apo-ArCP, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution30.25 mM [U-99% 13C; U-99% 15N] apo-ArCP, 100% D2O15N_13C_d2o_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMapo-ArCP[U-99% 15N]1
0.25 mMapo-ArCP[U-99% 13C; U-99% 15N]2
0.25 mMapo-ArCP[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDDetailsIonic strength unitsLabelpHPressure (kPa)Temperature (K)
1150 mM NaCl 1 mM MgCl2 0.5 mM TCEP 50 mM ACES 90% H2O/10% D2ONot definedH2O_Buffer6.81 atm298 K
2150 mM NaCl 1 mM MgCl2 0.5 mM TCEP 50 mM ACES 100% D2ONot definedD2O_Buffer6.4 pD1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy structure
NMR ensembleConformer selection criteria: lowest CYANA target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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