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- PDB-2my5: Solution Structure of KstB-PCP in kosinostatin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 2my5
TitleSolution Structure of KstB-PCP in kosinostatin biosynthesis
ComponentsPeptidyl carrier protein
KeywordsTRANSPORT PROTEIN / Ppant binnding domain
Function / homology
Function and homology information


ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PN7 / Peptidyl carrier protein
Similarity search - Component
Biological speciesMicromonospora sp. TP-A0468 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations and lowest energy, model1
AuthorsZhao, B. / Lan, W. / Wang, C. / Tang, G. / Cao, C.
CitationJournal: To be Published
Title: 1H and 15N Assigned Chemical Shifts for KstB-PCP
Authors: Zhao, B. / Lan, W. / Wang, C. / Tang, G. / Cao, C.
History
DepositionJan 20, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 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_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020
RepresentativeModel #1fewest violations and lowest 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) / Gene: KstB2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / 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 experimentType: 3D CBCA(CO)NH

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Sample preparation

DetailsContents: 2 mM [U-99% 13C; U-99% 15N] KstB-PCP(holo)-1, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: KstB-PCP(holo)-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionspH: 7 / Temperature units: K

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NMR measurement

NMR spectrometerType: AGILENT INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations and lowest energy
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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