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- PDB-2fax: CLOSTRIDIUM BEIJERINCKII FLAVODOXIN MUTANT: N137A OXIDIZED (150K) -

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Basic information

Entry
Database: PDB / ID: 2fax
TitleCLOSTRIDIUM BEIJERINCKII FLAVODOXIN MUTANT: N137A OXIDIZED (150K)
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN / FMN
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short 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
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLudwig, M.L. / Pattridge, K.A. / Metzger, A.L. / Dixon, M.M. / Eren, M. / Feng, Y. / Swenson, R.
Citation
Journal: Biochemistry / Year: 1997
Title: Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: the role of conformation changes.
Authors: Ludwig, M.L. / Pattridge, K.A. / Metzger, A.L. / Dixon, M.M. / Eren, M. / Feng, Y. / Swenson, R.P.
#1: Journal: Flavins and Flavoproteins 1993 : Proceedings of the Eleventh International Symposium, Nagoya (Japan) July 27-31, 1993
Year: 1994
Title: Cis-Trans Isomerization of the 57-58 Peptide in Crystalline Flavodoxins from C. Beijerinckii
Authors: Ludwig, M.L. / Dixon, M.M. / Pattridge, K.A. / Swenson, R.P.
#2: Journal: Chemistry and Biochemistry of Flavoenzymes / Year: 1992
Title: Structure and Redox Properties of Clostridial Flavodoxin
Authors: Ludwig, M.L. / Luschinsky, C.L.
#3: Journal: Flavins and Flavoproteins 1990 : Proceedings of the Tenth International Symposium, Como, Italy, July 15-20, 1990
Year: 1991
Title: Structural Characterization of Site Mutants of Clostridial Flavodoxin
Authors: Ludwig, M.L. / Pattridge, K.A. / Eren, M. / Swenson, R.P.
#4: Journal: Biochemistry / Year: 1990
Title: Structure and Oxidation-Reduction Behavior of 1-Deaza-Fmn Flavodoxins: Modulation of Redox Potentials in Flavodoxins
Authors: Ludwig, M.L. / Schopfer, L.M. / Metzger, A.L. / Pattridge, K.A. / Massey, V.
#5: Journal: J.Mol.Biol. / Year: 1977
Title: Structure of the Semiquinone Form of Flavodoxin from Clostridium Mp. Extension of 1.8 A Resolution and Some Comparisons with the Oxidized State
Authors: Smith, W.W. / Burnett, R.M. / Darling, G.D. / Ludwig, M.L.
#6: Journal: FLAVINS AND FLAVOPROTEINS / Year: 1976
Title: The Structure of Clostridium Mp Flavodoxin as a Function of Oxidation State, Some Comparisons of the Fmn-Binding Sites in Oxidized, Semiquinone and Reduced Forms
Authors: Ludwig, M.L. / Burnett, R.M. / Darling, G.D. / Jordan, S.R. / Kendall, D.S. / Smith, W.W.
#7: Journal: J.Biol.Chem. / Year: 1974
Title: The Structure of the Oxidized Form of Clostridial Flavodoxin at 1.9-A Resolution
Authors: Burnett, R.M. / Darling, G.D. / Kendall, D.S. / Lequesne, M.E. / Mayhew, S.G. / Smith, W.W. / Ludwig, M.L.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Structure of the Radical Form of Clostridial Flavodoxin: A New Molecular Model
Authors: Andersen, R.D. / Apgar, P.A. / Burnett, R.M. / Darling, G.D. / Lequesne, M.E. / Mayhew, S.G. / Ludwig, M.L.
#9: Journal: J.Biol.Chem. / Year: 1969
Title: The Structure of a Clostridial Flavodoxin. I. Crystallographic Characterization of the Oxidized and Semiquinone Forms
Authors: Ludwig, M.L. / Andersen, R.D. / Mayhew, S.G. / Massey, V.
History
DepositionDec 24, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7582
Polymers15,3011
Non-polymers4561
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.820, 60.820, 69.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein FLAVODOXIN


Mass: 15301.258 Da / Num. of mol.: 1 / Mutation: N137A
Source method: isolated from a genetically manipulated source
Details: OXIDIZED / Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Cell line: XL1-BLUE / Cell line (production host): XL1-BLUE / Production host: Escherichia coli (E. coli) / References: UniProt: P00322
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5-2.8 Mammonium sulfate1reservoir
2Tris-HCl1reservoiror phosphate

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceWavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 13973 / % possible obs: 99.3 % / Observed criterion σ(I): 0
Reflection
*PLUS
Rmerge(I) obs: 0.0525

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 13973 99.3 %
Displacement parametersBiso mean: 11.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 31 185 1286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.233
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.233

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