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- PDB-2k5f: Solution NMR structure of FeoA protein from Chlorobium tepidum. N... -

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Basic information

Entry
Database: PDB / ID: 2k5f
TitleSolution NMR structure of FeoA protein from Chlorobium tepidum. Northeast Structural Genomics Consortium target CtR121
ComponentsFerrous iron transport protein A
KeywordsMETAL TRANSPORT / SH3-like / alpha+beta / GFT / 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
Ferrous iron transport protein A
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodSOLUTION NMR / simulated annealing, simulated annealing in explicit water bath
AuthorsEletsky, A. / Sathyamoorthy, B. / Mills, J.L. / Zeri, A. / Zhao, L. / Hamilton, K. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. ...Eletsky, A. / Sathyamoorthy, B. / Mills, J.L. / Zeri, A. / Zhao, L. / Hamilton, K. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. / 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 FeoA protein from Chlorobium tepidum. Northeast Structural Genomics Consortium target CtR121
Authors: Eletsky, A. / Sathyamoorthy, B. / Mills, J.L. / Zeri, A. / Zhao, L. / Hamilton, K. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B.L. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 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: Ferrous iron transport protein A


Theoretical massNumber of molelcules
Total (without water)11,8731
Polymers11,8731
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 Ferrous iron transport protein A


Mass: 11872.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Genus: Chlorobium / Species: tepidum / Gene: feoA-2, CT0057 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8KGB1

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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 HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
181(4,3)D GFT (H)CCH-COSY ali
191(4,3)D GFT L-(H)CCH-COSY aro
11013D HNHA
11113D HNCO (hbond)
11213D 1H-15N,13Cali,13Caro NOESY
11322D 1H-13C CT-HSQC 28ms

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Sample preparation

Details
Solution-IDContentsSolvent system
11.26 mM [U-100% 13C; U-100% 15N] FeoA protein, 0.02 % sodium azide, 100 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.26 mM [U-5% 13C; U-100% 15N] FeoA protein, 0.02 % sodium azide, 100 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.26 mMFeoA protein[U-100% 13C; U-100% 15N]1
0.02 %sodium azide1
100 mMDTT1
5 mMcalcium chloride1
100 mMsodium chloride1
20 mMMES1
50 uMDSS1
1.26 mMFeoA protein[U-5% 13C; U-100% 15N]2
0.02 %sodium azide2
100 mMDTT2
5 mMcalcium chloride2
100 mMsodium chloride2
20 mMMES2
50 uMDSS2
Sample conditionsIonic strength: 115 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
XEASY1.3.13Bartels et al.data analysis
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSI2Wishat and Sykesdata analysis
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionevalidation
RefinementMethod: simulated annealing, simulated annealing in explicit water bath
Software ordinal: 1 / Details: CYANA 2.1, CNS 1.2
NMR constraintsNOE constraints total: 1583 / NOE intraresidue total count: 293 / NOE long range total count: 555 / NOE medium range total count: 295 / NOE sequential total count: 440 / Hydrogen bond constraints total count: 104 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 104 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.04 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.8 ° / Maximum upper distance constraint violation: 0.38 Å
NMR ensemble rmsDistance rms dev: 0.022 Å

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