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- PDB-2gdw: Solution structure of the B. brevis TycC3-PCP in A/H-state -

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Basic information

Entry
Database: PDB / ID: 2gdw
TitleSolution structure of the B. brevis TycC3-PCP in A/H-state
ComponentsTyrocidine synthetase III
KeywordsLIGASE/TRANSPORT PROTEIN / Three-helix bundle / LIGASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


amide biosynthetic process / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process
Similarity search - Function
ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-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 / Alpha/Beta hydrolase fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrocidine synthase 3
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodSOLUTION NMR / energy minimization
AuthorsKoglin, A. / Loehr, F. / Rogov, V.V. / Marahiel, M.A. / Bernhard, F. / Doetsch, V.
CitationJournal: Science / Year: 2006
Title: Conformational switches modulate protein interactions in peptide antibiotic synthetases
Authors: Koglin, A. / Mofid, M.R. / Loehr, F. / Schaefer, B. / Rogov, V.V. / Blum, M.-M. / Mittag, T. / Marahiel, M.A. / Bernhard, F. / Doetsch, V.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrocidine synthetase III


Theoretical massNumber of molelcules
Total (without water)9,2511
Polymers9,2511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrocidine synthetase III / Non-ribosomal peptide synthetase peptidyl carrier protein


Mass: 9250.676 Da / Num. of mol.: 1 / Fragment: Acyl carrier 3, TYCC3 THIOESTER DOMAIN / Mutation: P2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Strain: ATCC8185 / Gene: tycC / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: O30409

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM A/H-PCP U-15N; 50mM NaPi; 1mM TCEP; 95% H2O; 5% D2O95% H2O/5% D2O
20.8mM A/H-PCP; 50mM NaPi; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM NaPi; 1mM TCEP / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
XwinNMR2.6BRUKERprocessing
Sparky3.111Goddard & Knellerdata analysis
DYANA1.5Guentertstructure solution
GROMOS97van Gunsterenrefinement
RefinementMethod: energy minimization / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 19

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