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- PDB-2k5i: SOLUTION STRUCTURE OF IRON(II) TRANSPORT PROTEIN A FROM CLOSTRIDI... -

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Basic information

Entry
Database: PDB / ID: 2k5i
TitleSOLUTION STRUCTURE OF IRON(II) TRANSPORT PROTEIN A FROM CLOSTRIDIUM THERMOCELLUM , NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET VR131
ComponentsIRON TRANSPORT PROTEIN
KeywordsMETAL TRANSPORT / Iron(II) transport protein A / FeoA / Structural Genomic / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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
Iron transport protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodSOLUTION NMR / simulated annealing, distance geometry, torsion angle dynamics
AuthorsLiu, G. / Wang, H. / Foote, E.L. / Jiang, M. / Xiao, R. / Swapna, G. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Liu, G. / Wang, H. / Foote, E.L. / Jiang, M. / Xiao, R. / Swapna, G. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR chemical shift assignments of iron(ii) transport protein a from clostridium thermocellum , northeast structural genomics consortium (nesg) target vr131
Authors: Liu, g. / Xiao, r. / Montelione, G.T.
History
DepositionJun 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Data collection / Derived calculations / Structure summary
Category: pdbx_nmr_software / pdbx_nmr_spectrometer ...pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IRON TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,2771
Polymers18,2771
Non-polymers00
Water00
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 IRON TRANSPORT PROTEIN


Mass: 18277.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Species: thermocellum / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWX0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY
1313D SIMULTANEOUS CN-NOESY
1414,3D GFT CABCACONHN
1514,3D GFT HNNCABCA
1614,3D GFT HABCAB(CO)NHN
1713D CCH-COSY
1822D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.92 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.65 mM [U-10% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.92 mMprotein[U-100% 13C; U-100% 15N]1
0.65 mMprotein[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: na / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASY1.3.1Bartels et al.data analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
RefinementMethod: simulated annealing, distance geometry, torsion angle dynamics
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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