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- PDB-2kqu: F98N apoflavodoxin from Anabaena PCC 7119 -

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Basic information

Entry
Database: PDB / ID: 2kqu
TitleF98N apoflavodoxin from Anabaena PCC 7119
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / folding intermediate / Flavoprotein / FMN / Transport
Function / homology
Function and homology information


cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnabaena sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsAyuso-Tejedor, S. / Sancho, J. / Jimenez, M.A. / Bernado, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Design and structure of an equilibrium protein folding intermediate. A hint into dynamical regions of proteins
Authors: Ayuso-Tejedor, S. / Angarica, V.E. / Bueno, M. / Campos, L.A. / Abian, O. / Bernado, P. / Sancho, J. / Jimenez, M.A.
History
DepositionNov 19, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin


Theoretical massNumber of molelcules
Total (without water)18,7981
Polymers18,7981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Flavodoxin / / fdx


Mass: 18798.457 Da / Num. of mol.: 1 / Mutation: F98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC 7119 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3E0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1233D 1H-15N NOESY
1333D HNHA
1412D 1H-1H COSY
1512D 1H-1H TOCSY
1612D 1H-1H NOESY
1722D 1H-1H COSY
1822D 1H-1H TOCSY
1922D 1H-1H NOESY
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM F98N-fdx; 5mM sodium phosphate; 90% H2O; 10% D2O; 0.1mM DSS; 90% H2O/10% D2O90% H2O/10% D2O
21mM F98N-fdx; 5mM sodium phosphate; 100% D2O; 0.1mM DSS; 100% D2O100% D2O
31mM [U-15N] F98N-fdx; 5mM sodium phosphate; 90% H2O; 10% D2O; 0.1mM DSS; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMF98N-fdx-11
5 mMsodium phosphate-21
90 %H2O-31
10 %D2O-41
0.1 mMDSS-51
1 mMF98N-fdx-62
5 mMsodium phosphate-72
100 %D2O-82
0.1 mMDSS-92
1 mMF98N-fdx-10[U-15N]3
5 mMsodium phosphate-113
90 %H2O-123
10 %D2O-133
0.1 mMDSS-143
Sample conditionsIonic strength: 5 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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