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- PDB-2kf2: Solution NMR structure of of Streptomyces coelicolor polyketide c... -

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Basic information

Entry
Database: PDB / ID: 2kf2
TitleSolution NMR structure of of Streptomyces coelicolor polyketide cyclase SCO5315. Northeast Structural Genomics Consortium target RR365
ComponentsPutative polyketide cyclase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / aromatase/cyclase / ARO/CYC / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyCoenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Putative polyketide cyclase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailscombination of low energy, few restraint violations, good backbone geometry, model 1
AuthorsCort, J.R. / Ramelot, T.A. / Ding, K. / Wang, H. / Jiang, M. / Maglaqui, M. / Xiao, R. / Nair, R. / Baran, M.C. / Everett, J.K. ...Cort, J.R. / Ramelot, T.A. / Ding, K. / Wang, H. / Jiang, M. / Maglaqui, M. / Xiao, R. / Nair, R. / Baran, M.C. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Streptomyces coelicolor polyketide cyclase SCO5315
Authors: Cort, J.R.
History
DepositionFeb 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polyketide cyclase


Theoretical massNumber of molelcules
Total (without water)19,2741
Polymers19,2741
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 / 40lowest energy, fewest restraint violations, favorable backbone geometry
RepresentativeModel #1combination of low energy, few restraint violations, good backbone geometry

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Components

#1: Protein Putative polyketide cyclase


Mass: 19274.494 Da / Num. of mol.: 1 / Mutation: N20T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: A3(2) / M145 / Gene: SC6G9.18, SCO5315 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P23154
Sequence detailsTHE ENTITY WAS FOUND TO HAVE THR AT POSITION 20, WHEREAS THE TRANSLATED GENE SEQUENCE HAS ASN AT POSITION 20.

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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 HBHA(CO)NH
1613D HN(CO)CA
1713D HNCA
1813D H(CCO)NH
1913D C(CO)NH
11013D HNHA
11113D (H)CCH-TOCSY
11213D HNCO
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11524D-1H-13C-13C-1H HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] entity-1, 20 mM MES-2, 100 mM sodium chloride-3, 5 mM calcium chloride-4, 10 mM DTT-5, 50 uM DSS-6, 0.02 % sodium azide-7, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] entity-8, 20 mM MES-9, 100 mM sodium chloride-10, 5 mM calcium chloride-11, 10 mM DTT-12, 50 uM DSS-13, 0.02 % sodium azide-14, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
50 uMDSS-61
0.02 %sodium azide-71
1 mMentity-8[U-99% 13C; U-99% 15N]2
20 mMMES-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
50 uMDSS-132
0.02 %sodium azide-142
Sample conditionsIonic strength: 112 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX8502

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Processing

NMR software
NameDeveloperClassification
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
FelixFelix NMR Inc.data analysis
FelixFelix NMR Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PSVSBhattacharya and Montelionestructure solution
PSVSBhattacharya and Montelionedata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: combination of low energy, few restraint violations, good backbone geometry
NMR ensembleConformer selection criteria: lowest energy, fewest restraint violations, favorable backbone geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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