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- PDB-5z4f: An anthrahydroquino-Gama-pyrone synthase Txn09 complexed with SUM -

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Basic information

Entry
Database: PDB / ID: 5z4f
TitleAn anthrahydroquino-Gama-pyrone synthase Txn09 complexed with SUM
ComponentsTxnO9
KeywordsBIOSYNTHETIC PROTEIN / type II polyketide heterocyclase / enzyme mechanism / natural product / Streptomyces bottropensis
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / Chem-96F / TxnO9
Function and homology information
Biological speciesStreptomyces bottropensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSong, Y.J. / Cao, C.Y.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Enzymology of Anthraquinone-gamma-Pyrone Ring Formation in Complex Aromatic Polyketide Biosynthesis.
Authors: Hou, X.F. / Song, Y.J. / Zhang, M. / Lan, W.X. / Meng, S. / Wang, C.X. / Pan, H.X. / Cao, C.Y. / Tang, G.L.
History
DepositionJan 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: 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 1.2May 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: TxnO9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2342
Polymers17,8381
Non-polymers3961
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 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 TxnO9 / anthrahydroquino-Gama-pyrone synthase


Mass: 17837.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bottropensis (bacteria) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A0K1H313
#2: Chemical ChemComp-96F / 1,8-dihydroxy-2-[(4R)-4-hydroxy-4-methyl-3-oxohexanoyl]-3-methylanthracene-9,10-dione


Mass: 396.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20O7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
161isotropic22D 1H-15N HSQC
171isotropic22D 1H-13C HSQC aliphatic
181isotropic22D 1H-13C HSQC aromatic
191isotropic23D (H)CCH-TOCSY
1101isotropic23D 1H-15N TOCSY
1111isotropic23D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY aliphatic
1131isotropic23D 1H-13C NOESY aromatic
1141isotropic12D filtered NOESY
1151isotropic12D filtered TOCSY
1161isotropic13D edited/filtered NOESY

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-99% 13C; U-99% 15N] Txn09, 50 mM sodium chloride, 20 mM sodium phosphate, 10 % v/v Deuteration DMSO, 90% H2O/10% D2O
Details: 10%DMSO / Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMTxn09[U-99% 13C; U-99% 15N]1
50 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
10 % v/vDMSODeuteration1
Sample conditionsIonic strength: 60 mM / Label: condition-1 / pH: 7.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD26001
Agilent DD2AgilentDD28002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
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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