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- PDB-6tdm: Bam_5920cDD 5919nDD docking domains -

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Basic information

Entry
Database: PDB / ID: 6tdm
TitleBam_5920cDD 5919nDD docking domains
ComponentsBeta-ketoacyl synthase,Beta-ketoacyl synthase
KeywordsPROTEIN BINDING / docking domain / polyketide synthase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal 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 ...Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal 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 / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / Phosphopantetheine attachment site / Thiolase-like / 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
Beta-ketoacyl synthase / Beta-ketoacyl synthase
Similarity search - Component
Biological speciesBurkholderia ambifaria AMMD (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRisser, F. / Chagot, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase.
Authors: Risser, F. / Collin, S. / Dos Santos-Morais, R. / Gruez, A. / Chagot, B. / Weissman, K.J.
History
DepositionNov 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketoacyl synthase,Beta-ketoacyl synthase
B: Beta-ketoacyl synthase,Beta-ketoacyl synthase


Theoretical massNumber of molelcules
Total (without water)13,4692
Polymers13,4692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2780 Å2
ΔGint-21 kcal/mol
Surface area8860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Beta-ketoacyl synthase,Beta-ketoacyl synthase


Mass: 6734.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria AMMD (bacteria) / Gene: Bamb_5920, Bamb_5919 / Plasmid: pBG102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0B308, UniProt: Q0B309

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HNCO
141isotropic13D CBCA(CO)NH
1131isotropic13D HN(CA)CB
1121isotropic13D (H)CCH-TOCSY
1111isotropic13D H(CCO)NH
1101isotropic13D C(CO)NH
191isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 25

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