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- PDB-2lml: Solution NMR structure of holo acyl carrier protein from geobacte... -

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Basic information

Entry
Database: PDB / ID: 2lml
TitleSolution NMR structure of holo acyl carrier protein from geobacter Metallireducens refined with nh rdcs, Northeast Structural Genomics consortium target gmr141
ComponentsPutative acyl carrier protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha / 4'-PHOSPHOPANTETHEINE / Acyl carrier protein
Function and homology information
Biological speciesGeobacter metallireducens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Smola, M.J. / Lee, H. / Zhao, L. / Ciccosanti, C. / Foote, E.L. / Hamilton, K. / Nair, R. / Rost, B. / Swapna, G. ...Ramelot, T.A. / Smola, M.J. / Lee, H. / Zhao, L. / Ciccosanti, C. / Foote, E.L. / Hamilton, K. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Biochemistry / Year: 2011
Title: Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis.
Authors: Ramelot, T.A. / Smola, M.J. / Lee, H.W. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 5, 2011Deposition site: BMRB / Processing site: RCSB
SupersessionJan 25, 2012ID: 2KWM
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3832
Polymers10,0241
Non-polymers3581
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative acyl carrier protein


Mass: 10024.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / ATCC 53774 / DSM 7210 / Description: GmR141-21.1 / Gene: Gmet_2339 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39T60
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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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 aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1532D 1H-13C HSQC
1622D 1H-13C HSQC-CT
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliph
1913D HNCO
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D 1H-13C NOESY arom
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D C(CCO)NH
11633D (H)CCH-COSY
11713D (H)CCH-TOCSY
11833D CCH-TOCSY
11934D CC-NOESY
12012D 1H-13C HSQC aromatic
12122D 1H-15N hetNOE
12222D 1H-15N HSQC His

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM U-100% 15N and 5% 13C biosynthetically directed protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
10 mMDTT-61
1.0 mMprotein-7U-100% 15N and 5% 13C biosynthetically directed2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.0 mMprotein-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
0.02 %sodium azide-173
10 mMDTT-183
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.4(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
FMCGUIAlex Lemak, University of Torontorefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement (via fmcGui) + RDCs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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