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- PDB-1dny: SOLUTION STRUCTURE OF PCP, A PROTOTYPE FOR THE PEPTIDYL CARRIER D... -

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Basic information

Entry
Database: PDB / ID: 1dny
TitleSOLUTION STRUCTURE OF PCP, A PROTOTYPE FOR THE PEPTIDYL CARRIER DOMAINS OF MODULAR PEPTIDE SYNTHETASES
ComponentsNON-RIBOSOMAL PEPTIDE SYNTHETASE PEPTIDYL CARRIER PROTEIN
KeywordsLIGASE / FOUR-HELIX BUNDLE / MODULAR ENZYME / FLEXIBLE REGION / 4'-PHOSPHOPANTETHEINYL COFACTOR / modular peptide synthetases / nonribosomal peptide synthesis / peptidyl carrier protein (PCP)
Function / homology
Function and homology information


amide biosynthetic process / secondary metabolite biosynthetic process / organonitrogen compound 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 brevis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsWeber, T. / Baumgartner, R. / Renner, C. / Marahiel, M.A. / Holak, T.A.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Solution structure of PCP, a prototype for the peptidyl carrier domains of modular peptide synthetases.
Authors: Weber, T. / Baumgartner, R. / Renner, C. / Marahiel, M.A. / Holak, T.A.
History
DepositionDec 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NON-RIBOSOMAL PEPTIDE SYNTHETASE PEPTIDYL CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,1201
Polymers10,1201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein NON-RIBOSOMAL PEPTIDE SYNTHETASE PEPTIDYL CARRIER PROTEIN


Mass: 10119.620 Da / Num. of mol.: 1 / Fragment: TYCC3 THIOESTER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: TYCC / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / References: UniProt: O30409

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1242D NOESY
1323D 15N-separated NOESY
1433D 13C-separated NOESY
152HNHA
NMR detailsText: All spectrometers were equipped with triple resonance (1H, 13C, 15N) probeheads and pulsed-field gradient accessories. The structure was determined using triple-resonance NMR techniques. BEST ...Text: All spectrometers were equipped with triple resonance (1H, 13C, 15N) probeheads and pulsed-field gradient accessories. The structure was determined using triple-resonance NMR techniques. BEST REPRESENTATIVE CONFORMER 1 IN THIS ENSEMBLE is the minimized mean structure of the remaining 20 conformers.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM PCP; 50 mM Na-phosphate buffer pH 5.0590% H2O/10% D2O
21.8 mM PCP U-15N; 50 mM Na-phosphate buffer pH 5.0590% H2O/10% D2O
31.8 mM PCP U-15N,13C; 50 mM Na-phosphate buffer pH 5.05100% D2O
41.8 mM PCP; 50 mM Na-phosphate buffer pH 5.05100% D2O
Sample conditionsIonic strength: 50 mM Na-Phosphate / pH: 5.05 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX6003
Bruker DMXBrukerDMX7504

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Processing

NMR software
NameVersionDeveloperClassification
CC-NMRCieslarrefinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: USED DISTANCE CONSTRAINTS: 856; intra-residue: 47; sequential: 287; medium range (2<|i-j|<5): 215; long range (|i-j|>4): 253; hydrogen bonds (2 restraints per H-bond): 54;DIHEDRAL ANGLE CONSTRAINTS: 104
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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