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- PDB-1fdr: FLAVODOXIN REDUCTASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1fdr
TitleFLAVODOXIN REDUCTASE FROM E. COLI
ComponentsFLAVODOXIN REDUCTASE
KeywordsFLAVOPROTEIN / FLAVODOXIN REDUCTASE / FERREDOXIN REDUCTASE / FLAVIN / OXIDOREDUCTASE
Function / homology
Function and homology information


flavodoxin-NADP+ reductase / aconitate hydratase activity / succinate dehydrogenase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / response to superoxide / iron-sulfur cluster assembly / FAD binding / cellular response to oxidative stress ...flavodoxin-NADP+ reductase / aconitate hydratase activity / succinate dehydrogenase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / response to superoxide / iron-sulfur cluster assembly / FAD binding / cellular response to oxidative stress / response to xenobiotic stimulus / cytosol
Similarity search - Function
Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain ...Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsIngelman, M. / Bianchi, V. / Eklund, H.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 A resolution.
Authors: Ingelman, M. / Bianchi, V. / Eklund, H.
History
DepositionMar 6, 1997Processing site: BNL
Revision 1.0Sep 17, 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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVODOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5992
Polymers27,8131
Non-polymers7861
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.130, 51.100, 40.670
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FLAVODOXIN REDUCTASE / FERREDOXIN REDUCTASE


Mass: 27812.979 Da / Num. of mol.: 1 / Mutation: R126Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 C600 / Cellular location: CYTOPLASM / Gene: FPR / Plasmid: PEE1010 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): S30 / References: UniProt: P28861, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.3 / Details: 1.2 M SODIUM CITRATE 100MM TRISHCL PH 7.3
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21.2 Msodium citrate1reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 8, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 28503 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rsym value: 0.064 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→2 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.23 / % possible all: 29
Reflection
*PLUS
Num. measured all: 68969 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 29 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -7 %RANDOM
Rwork0.184 ---
obs0.184 19171 --
Displacement parametersBiso mean: 18.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 53 206 2208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
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
LS refinement shellResolution: 1.7→1.87 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 -7 %
Rwork0.29 1200 -
obs--30 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.5
LS refinement shell
*PLUS
Rfactor obs: 0.29

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