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- PDB-1nq4: Solution Structure of Oxytetracycline Acyl Carrier Protein -

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Basic information

Entry
Database: PDB / ID: 1nq4
TitleSolution Structure of Oxytetracycline Acyl Carrier Protein
ComponentsOxytetracycline polyketide synthase acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / solution structure / oxytetracycline / polyketide synthase / dynamics / ACP
Function / homology
Function and homology information


antibiotic biosynthetic process
Similarity search - Function
ACP-like / 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
Oxytetracycline polyketide synthase acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces rimosus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsFindlow, S.C. / Winsor, C. / Simpson, T.J. / Crosby, J. / Crump, M.P.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure and dynamics of oxytetracycline polyketide synthase acyl carrier protein from Streptomyces rimosus
Authors: Findlow, S.C. / Winsor, C. / Simpson, T.J. / Crosby, J. / Crump, M.P.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxytetracycline polyketide synthase acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,9231
Polymers9,9231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 60low energy conformers with no NOE violations exceeding 0.3A
RepresentativeModel #1closest to the average

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Components

#1: Protein Oxytetracycline polyketide synthase acyl carrier protein


Mass: 9922.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimosus (bacteria) / Gene: otcY1-3 / Plasmid: pT-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P43677

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
141DQF-COSY
151HNHA
1611H-15N HSQC
1713D 15N-separated TOCSY

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Sample preparation

DetailsContents: 2mM otc ACP U-15N; 20mM acetate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.15 / pH: 5.3 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglioprocessing
PIPPDan Garrettdata analysis
X-PLORAlex T Brungerstructure solution
X-PLORAlex T Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structures are based on a total of 1131 restraints, 1054 are NOE-derived distance constraints, 77 dihedral angle restraints,76 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: low energy conformers with no NOE violations exceeding 0.3A
Conformers calculated total number: 60 / Conformers submitted total number: 28

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