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- PDB-2k5l: Solution NMR Structure of Protein FeoA from Clostridium thermocel... -

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Basic information

Entry
Database: PDB / ID: 2k5l
TitleSolution NMR Structure of Protein FeoA from Clostridium thermocellum, Northeast Structural Genomics Consortium Target CmR17
ComponentsFeoA
Keywordsstructural genomics / unknown function / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


transition metal ion binding
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / Transcriptional repressor, C-terminal / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium thermocellum ATCC 27405 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZeri, A. / Singarapu, K.K. / Mills, J.L. / Wu, Y. / Garcia, E. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. ...Zeri, A. / Singarapu, K.K. / Mills, J.L. / Wu, Y. / Garcia, E. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Protein FeoA from Clostridium thermocellum, Northeast Structural Genomics Consortium Target CmR17
Authors: Zeri, A. / Singarapu, K.K. / Mills, J.L. / Wu, Y. / Garcia, E. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / ...Authors: Zeri, A. / Singarapu, K.K. / Mills, J.L. / Wu, Y. / Garcia, E. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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 8, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FeoA


Theoretical massNumber of molelcules
Total (without water)9,2481
Polymers9,2481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein FeoA


Mass: 9247.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Species: thermocellum / Gene: Cthe_0619 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: A3DD25

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-13C HSQC
1212D 1H-15N HSQC
1313D HNCO
141GFT (4,3)D (H)CCH COSY
151GFT (4,3)D simNOESY
161GFT (4,3)D HNCABCA
171GFT (4,3)D CABCACONH
181GFT (4,3)D HABCAB(CO)NHN

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-10% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMprotein[U-100% 13C; U-100% 15N]1
1.2 mMprotein[U-10% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.5 6.5 ambient 298 K
20.5 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
MOLMOLKoradi, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SPSCANGlaserprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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