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- PDB-5vj7: Ferredoxin NADP Oxidoreductase (Xfn) -

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Basic information

Entry
Database: PDB / ID: 5vj7
TitleFerredoxin NADP Oxidoreductase (Xfn)
Components
  • Ferredoxin-NADP(+) reductase subunit alpha
  • Oxidoreductase
KeywordsOXIDOREDUCTASE / Archaea / Hyperthermophile / Electron bifurcation / NfnII / Metabolism / sulfur
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / pyrimidine nucleotide biosynthetic process / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Glutamate synthase (NADPH), homotetrameric / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD-binding domain, ferredoxin reductase-type ...Glutamate synthase (NADPH), homotetrameric / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin-NADP(+) reductase subunit alpha / Oxidoreductase
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZadvornyy, O.A. / Nguyen, D.M.N. / Schut, G.J. / Lipscomb, G.L. / Tokmina-Lukaszewska, M. / Adams, M.W.W. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012518 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Two functionally distinct NADP(+)-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus.
Authors: Nguyen, D.M.N. / Schut, G.J. / Zadvornyy, O.A. / Tokmina-Lukaszewska, M. / Poudel, S. / Lipscomb, G.L. / Adams, L.A. / Dinsmore, J.T. / Nixon, W.J. / Boyd, E.S. / Bothner, B. / Peters, J.W. / Adams, M.W.W.
History
DepositionApr 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Ferredoxin-NADP(+) reductase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8258
Polymers85,3502
Non-polymers2,4756
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-105 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.743, 73.140, 99.963
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Oxidoreductase /


Mass: 52571.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_09035 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6V148
#2: Protein Ferredoxin-NADP(+) reductase subunit alpha


Mass: 32778.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_09030 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6TYZ3, ferredoxin-NADP+ reductase

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Non-polymers , 5 types, 191 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.22 Magnesium Sulfate, 27% w/v Polyethylene glycol 3,350, 0.4% v/v Ethyl acetate 1 mM Sodium dithionite

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.55→39 Å / Num. obs: 25850 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3147 / CC1/2: 0.934 / Rpim(I) all: 0.306 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
Aimless0.5.28data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFC

5jfc


Resolution: 2.55→39 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.814 / SU R Cruickshank DPI: 1.354 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.063 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.314
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1226 4.74 %RANDOM
Rwork0.183 ---
obs0.186 25850 98.6 %-
Displacement parametersBiso mean: 44.63 Å2
Baniso -1Baniso -2Baniso -3
1-22.2376 Å20 Å2-10.2418 Å2
2--6.9072 Å20 Å2
3----29.1449 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.55→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 0 127 186 6216
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016225HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198503HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2196SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it6225HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion19.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion794SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7223SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.65 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3266 151 5.18 %
Rwork0.2032 2764 -
all0.2098 2915 -
obs--99.01 %

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