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- PDB-5u3h: Solution structure of apo PCP1 from yersiniabactin synthetase -

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Basic information

Entry
Database: PDB / ID: 5u3h
TitleSolution structure of apo PCP1 from yersiniabactin synthetase
ComponentsHMWP2 nonribosomal peptide synthetase
KeywordsLIGASE / peptidyl carrier protein / NRPS
Function / homology
Function and homology information


toxin biosynthetic process / 2,3-dihydroxybenzoate-serine ligase activity / amide biosynthetic process / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / acyl carrier activity / catalytic activity / cytoplasm
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain ...Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-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, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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
Yersiniabactin biosynthetic protein / Yersiniabactin biosynthetic protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsHarden, B.J. / Frueh, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM 104257 United States
CitationJournal: Chembiochem / Year: 2017
Title: Molecular Cross-Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions.
Authors: Harden, B.J. / Frueh, D.P.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5May 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: HMWP2 nonribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)12,3541
Polymers12,3541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein HMWP2 nonribosomal peptide synthetase / Yersiniabactin biosynthetic protein


Mass: 12353.520 Da / Num. of mol.: 1 / Fragment: UNP residues 1383-1491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: irp2, y2399, YPO1911 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CI41, UniProt: A0A3N4B635*PLUS

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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
132isotropic13D HNCO
142isotropic13D HN(CA)CO
152isotropic13D HN(CO)CA
182isotropic13D HNCA
162isotropic13D HN(COCA)CB
172isotropic13D HN(CA)CB
1122isotropic13D H(CCCO)NH
1132isotropic13D (H)C(CCO)NH
1142isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY-HSQC
1103isotropic13D 1H-13C HSQC-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1920 uM protein, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 400 uM DSS, 95% H2O/5% D2O15N95% H2O/5% D2O
solution21.4 mM protein, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 400 uM DSS, 95% H2O/5% D2O15N_13C95% H2O/5% D2O
solution31.4 mM protein, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 400 uM DSS, 100% D2O15N_13C_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
1 mMDTTnatural abundance1
400 uMDSSnatural abundance1
20 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
1 mMEDTAnatural abundance2
1 mMDTTnatural abundance2
400 uMDSSnatural abundance2
20 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
1 mMEDTAnatural abundance3
1 mMDTTnatural abundance3
400 uMDSSnatural abundance3
Sample conditionsIonic strength: 200 mM / Label: conditions / pH: 6.60 / Pressure: 1 atm / Temperature: 298 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
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 4 / Details: simulated annealing
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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