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- PDB-5wpy: Solution Structure of KstB-PCP loaded with nicotinic acid in kosi... -

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Basic information

Entry
Database: PDB / ID: 5wpy
TitleSolution Structure of KstB-PCP loaded with nicotinic acid in kosinostatin biosynthesis
ComponentsPeptidyl carrier protein
KeywordsTRANSPORT PROTEIN / NRPS
Function / homologyPhosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Chem-PN7 / Peptidyl carrier protein
Function and homology information
Biological speciesMicromonospora sp. TP-A0468 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhao, B. / Lan, W. / Tang, G. / Cao, C.
CitationJournal: To Be Published
Title: major solution Structure of KstB-PCP in kosinostatin biosynthesis
Authors: Zhao, B. / Lan, W. / Tang, G. / Cao, C.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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 / _pdbx_nmr_software.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0232
Polymers9,6651
Non-polymers3581
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6080 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl carrier protein


Mass: 9664.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. TP-A0468 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023GUP0
#2: Chemical ChemComp-PN7 / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
Has protein modificationY

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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
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HNCA
191isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 2.0 mM [U-99% 15N][U-99% 13C] holo-KstB-PCP, 80 mM sodium phosphate, 50 mM NaCl, 90% H2O/10% D2O
Label: 15N_13C_KstB-PCP / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMholo-KstB-PCP[U-99% 15N][U-99% 13C]1
80 mMsodium phosphatenatural abundance1
50 mMNaClnatural abundance1
Sample conditionsIonic strength: 130 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJANDRA AND CLORErefinement
X-PLOR NIHstructure solution
Sparkystructure solution
NMRPipestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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