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- PDB-5y08: Solution structure of the apo doublet acyl carrier protein from p... -

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Basic information

Entry
Database: PDB / ID: 5y08
TitleSolution structure of the apo doublet acyl carrier protein from prodigiosin biosynthesis
Components4-hydroxy-2,2'-bipyrrole-5-methanol synthase PigH
KeywordsBIOSYNTHETIC PROTEIN / acyl carrier protein
Function / homology
Function and homology information


pyridoxal binding / Transferases; Acyltransferases; Aminoacyltransferases / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding / membrane
Similarity search - Function
Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain ...Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
4-hydroxy-2,2'-bipyrrole-5-methanol synthase PigH
Similarity search - Component
Biological speciesSerratia sp. ATCC 39006 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWattana-amorn, P.
Funding support United Kingdom, Thailand, 3items
OrganizationGrant numberCountry
BrisSynBio BB/L01386X/1 United Kingdom
Kasetsart University RFG1-7/2558 Thailand
Biotechnology and Biological Sciences Research CouncilBB/F014570/1 United Kingdom
CitationJournal: Biochemistry / Year: 2021
Title: Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.
Authors: Thongkawphueak, T. / Winter, A.J. / Williams, C. / Maple, H.J. / Soontaranon, S. / Kaewhan, C. / Campopiano, D.J. / Crump, M.P. / Wattana-Amorn, P.
History
DepositionJul 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
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:
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Assembly

Deposited unit
A: 4-hydroxy-2,2'-bipyrrole-5-methanol synthase PigH


Theoretical massNumber of molelcules
Total (without water)22,2241
Polymers22,2241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein 4-hydroxy-2,2'-bipyrrole-5-methanol synthase PigH / HBM synthase / Aminotransferase PigH


Mass: 22223.814 Da / Num. of mol.: 1 / Fragment: UNP residues 1-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. ATCC 39006 / Strain: ATCC 39006 / Gene: pigH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5W264, Transferases; Acyltransferases; Aminoacyltransferases

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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
121isotropic13D HNCA
171isotropic13D HN(CO)CA
161isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
141isotropic13D HNCO
131isotropic13D C(CO)NH
1101isotropic13D H(CCO)NH
191isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY
1121isotropic13D 1H-13C NOESY aromatic
NMR detailsText: refinement in explicit water using RECOORD protocol

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Sample preparation

DetailsType: solution
Contents: 20 mM None TRIS, 5 mM None DTT, 0.1 mM None sodium azide, 90% H2O/10% D2O
Label: PigHACP1ACP2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISNone1
5 mMDTTNone1
0.1 mMsodium azideNone1
Sample conditionsIonic strength: 0.1 mM NaN3 Not defined / Label: PigHACP_condition / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz / Details: equipped with cryo-probe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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