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- PDB-2n5d: NMR structure of PKS domains -

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Basic information

Entry
Database: PDB / ID: 2n5d
TitleNMR structure of PKS domains
Componentsfusion protein of two PKS domains
KeywordsPROTEIN BINDING / docking domain / polyketide synthase
Function / homology
Function and homology information


amide biosynthetic process / toxin biosynthetic process / : / : / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process ...amide biosynthetic process / toxin biosynthetic process / : / : / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Condensation domain / Condensation domain ...: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Hybrid polyketide synthase-non ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsDorival, J. / Annaval, T. / Risser, F. / Collin, S. / Roblin, P. / Jacob, C. / Gruez, A. / Chagot, B. / Weissman, K.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase.
Authors: Dorival, J. / Annaval, T. / Risser, F. / Collin, S. / Roblin, P. / Jacob, C. / Gruez, A. / Chagot, B. / Weissman, K.J.
History
DepositionJul 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: fusion protein of two PKS domains


Theoretical massNumber of molelcules
Total (without water)8,4551
Polymers8,4551
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein fusion protein of two PKS domains


Mass: 8455.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virA / Plasmid: pBG102 (pet27 derivative) / Production host: Escherichia coli (E. coli) / References: UniProt: A4PHN0
Sequence detailsRESIDUES 50-84 CORRESPOND TO A SECOND PKS DOMAIN THAT HAS NO UNIPROT SEQUENCE REFERENCE AT THE TIME ...RESIDUES 50-84 CORRESPOND TO A SECOND PKS DOMAIN THAT HAS NO UNIPROT SEQUENCE REFERENCE AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.115Goddardchemical shift assignment
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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