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- PDB-5mti: Bamb_5917 Acyl-Carrier Protein -

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Basic information

Entry
Database: PDB / ID: 5mti
TitleBamb_5917 Acyl-Carrier Protein
ComponentsPhosphopantetheine-binding protein
KeywordsTRANSPORT PROTEIN / Peptidyl Carrier Protein / Polyketides Synthases / NRPS / NMR Structural Biology
Function / homologyPolyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / phosphopantetheine binding / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Phosphopantetheine-binding protein
Function and homology information
Biological speciesBurkholderia ambifaria AMMD (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsGallo, A. / Kosol, S. / Griffiths, D. / Masschelein, J. / Alkhalaf, L. / Smith, H. / Valentic, T. / Tsai, S. / Challis, G. / Lewandowski, J.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L022761/1 United Kingdom
European Union639907 United Kingdom
CitationJournal: Nat.Chem. / Year: 2019
Title: Structural basis for chain release from the enacyloxin polyketide synthase
Authors: Griffiths, D. / Gallo, A. / Kosol, S. / Valentic, T. / Smith, H. / Alkhalaf, L. / Masschelein, J. / Tsai, S. / Challis, G. / Lewandowski, J.R.
History
DepositionJan 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Feb 12, 2020Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine-binding protein


Theoretical massNumber of molelcules
Total (without water)11,3241
Polymers11,3241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Phosphopantetheine-binding protein


Mass: 11323.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Stretch of the full protein sequence from residues 215 to 315 GIDPFT TEV cleavage site
Source: (gene. exp.) Burkholderia ambifaria AMMD (bacteria) / Gene: Bamb_5917 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0B311

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic13D 1H-15N NOESY
132isotropic13D 1H-13C NOESY
142isotropic13D HNCO
152isotropic13D HN(CA)CO
162isotropic13D HNCA
172isotropic13D HN(CO)CA
182isotropic13D HN(CA)CB
192isotropic13D HN(COCA)CB
1102isotropic13D HBHA(CO)NH
1112isotropic13D (H)CCH-TOCSY
1121isotropic12D 1H-15N HSQC
1132isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] 15N_PCP17, 50 mM potassium phosphate, 200 mM sodium chloride, 1 % DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O15N_Sample90% H2O/10% D2O
solution20.3 mM [U-13C; U-15N] 13C,15N_PCP17, 50 mM potassium phosphate, 200 mM sodium chloride, 1 % DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O13C,15N_Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM15N_PCP17[U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
200 mMsodium chloridenatural abundance1
1 %DSSnatural abundance1
90 %H2Onatural abundance1
10 %D2Onatural abundance1
0.3 mM13C,15N_PCP17[U-13C; U-15N]2
50 mMpotassium phosphatenatural abundance2
200 mMsodium chloridenatural abundance2
1 %DSSnatural abundance2
90 %H2Onatural abundance2
10 %D2Onatural abundance2
Sample conditionsIonic strength: 250 mM / Label: condition_1 / pH: 6.50 / PH err: 0.05 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: cryo probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5pl6Bruker Biospincollection
TopSpin3.5pl6Bruker Biospinprocessing
CARA3Keller and Wuthrichdata analysis
CARA3Keller and Wuthrichchemical shift assignment
ATNOS/CANDIDUNIOHerrmann, Guntert and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
Details: The 20 conformers of apo-PCP17 with the lowest target function values were subjected to restrained energy minimization and Molecular Dynamics (MD) calculations in explicit solvent with AMBER ...Details: The 20 conformers of apo-PCP17 with the lowest target function values were subjected to restrained energy minimization and Molecular Dynamics (MD) calculations in explicit solvent with AMBER 14.0. NOEs and torsion angle constraints were applied with force constants of 50 kcal mol?1??2 and 32 kcal mol?1 rad?2, respectively.
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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