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- PDB-5jca: NADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI... -

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Basic information

Entry
Database: PDB / ID: 5jca
TitleNADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus
Components(NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit ...) x 2
KeywordsOXIDOREDUCTASE / NfnI / Pyrococcus furiosus / NADP(H) bound NfnI
Function / homology
Function and homology information


sulfide dehydrogenase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / pyrimidine nucleotide biosynthetic process / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
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 / Chem-NDP / IRON/SULFUR CLUSTER / Sulfide dehydrogenase subunit beta / Sulfide dehydrogenase subunit alpha
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZadvornyy, O.A. / Schut, G.J. / Nguyen, D.M. / Artz, J.H. / Tokmina-Lukaszewska, M. / Lipscomb, G. / Adams, M.W. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012518 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Mechanistic insights into energy conservation by flavin-based electron bifurcation.
Authors: Lubner, C.E. / Jennings, D.P. / Mulder, D.W. / Schut, G.J. / Zadvornyy, O.A. / Hoben, J.P. / Tokmina-Lukaszewska, M. / Berry, L. / Nguyen, D.M. / Lipscomb, G.L. / Bothner, B. / Jones, A.K. / ...Authors: Lubner, C.E. / Jennings, D.P. / Mulder, D.W. / Schut, G.J. / Zadvornyy, O.A. / Hoben, J.P. / Tokmina-Lukaszewska, M. / Berry, L. / Nguyen, D.M. / Lipscomb, G.L. / Bothner, B. / Jones, A.K. / Miller, A.F. / King, P.W. / Adams, M.W.W. / Peters, J.W.
History
DepositionApr 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha
S: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,66610
Polymers84,3542
Non-polymers3,3128
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-103 kcal/mol
Surface area29090 Å2
MethodPISA
2
L: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha
S: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta
hetero molecules

L: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha
S: NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,33220
Polymers168,7084
Non-polymers6,62416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area21050 Å2
ΔGint-220 kcal/mol
Surface area55730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.681, 179.681, 80.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit ... , 2 types, 2 molecules LS

#1: Protein NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha / SuDH / Ferredoxin:NADP oxidoreductase / FNOR


Mass: 52802.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U195, EC: 1.6.1.4
#2: Protein NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta / SuDH / Ferredoxin:NADP oxidoreductase / FNOR


Mass: 31550.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U194, EC: 1.6.1.4

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Non-polymers , 7 types, 1049 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 4.54 Å3/Da / Density % sol: 72.92 % / Description: rod shape crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 2.5 M Ammonium formate, 20% Glycerol / PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.5→47.52 Å / Num. obs: 237751 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 12.66 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 30.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.71 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
HKL-2000v712data reduction
SCALAv712data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→47.525 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1528 11765 5.01 %
Rwork0.1386 --
obs0.1393 234804 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→47.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 181 1043 7074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146160
X-RAY DIFFRACTIONf_angle_d1.6558356
X-RAY DIFFRACTIONf_dihedral_angle_d19.7062353
X-RAY DIFFRACTIONf_chiral_restr0.098926
X-RAY DIFFRACTIONf_plane_restr0.0081048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4998-1.51680.23473240.21265902X-RAY DIFFRACTION79
1.5168-1.53470.21453380.19726752X-RAY DIFFRACTION91
1.5347-1.55340.19963620.18777258X-RAY DIFFRACTION97
1.5534-1.5730.18963760.17937385X-RAY DIFFRACTION99
1.573-1.59370.18213840.16917496X-RAY DIFFRACTION100
1.5937-1.61560.17493810.16427551X-RAY DIFFRACTION100
1.6156-1.63870.18554000.16567421X-RAY DIFFRACTION100
1.6387-1.66310.18483940.15547532X-RAY DIFFRACTION100
1.6631-1.68910.1573890.14857475X-RAY DIFFRACTION100
1.6891-1.71680.18013870.14877511X-RAY DIFFRACTION100
1.7168-1.74640.15354650.14347437X-RAY DIFFRACTION100
1.7464-1.77820.15454570.14357430X-RAY DIFFRACTION100
1.7782-1.81240.14563480.13727523X-RAY DIFFRACTION100
1.8124-1.84940.15233830.13877490X-RAY DIFFRACTION100
1.8494-1.88960.15723940.13597523X-RAY DIFFRACTION100
1.8896-1.93350.15014370.1367495X-RAY DIFFRACTION100
1.9335-1.98190.15093840.1327507X-RAY DIFFRACTION100
1.9819-2.03550.15823770.1337515X-RAY DIFFRACTION100
2.0355-2.09540.14594450.13237461X-RAY DIFFRACTION100
2.0954-2.1630.14253850.12657544X-RAY DIFFRACTION100
2.163-2.24030.14743910.12797542X-RAY DIFFRACTION100
2.2403-2.330.14374550.12397426X-RAY DIFFRACTION100
2.33-2.4360.14253500.12857634X-RAY DIFFRACTION100
2.436-2.56450.1424290.13047460X-RAY DIFFRACTION100
2.5645-2.72510.15223650.13597584X-RAY DIFFRACTION100
2.7251-2.93550.15193320.13997608X-RAY DIFFRACTION100
2.9355-3.23090.1624330.14667573X-RAY DIFFRACTION100
3.2309-3.69820.14454160.13267560X-RAY DIFFRACTION100
3.6982-4.65870.12483640.11817662X-RAY DIFFRACTION100
4.6587-47.54880.15444200.14537782X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -60.439 Å / Origin y: 64.9523 Å / Origin z: 9.7878 Å
111213212223313233
T0.0716 Å2-0.019 Å2-0.0169 Å2-0.1117 Å20.0081 Å2--0.0687 Å2
L0.4299 °20.4087 °2-0.1452 °2-0.883 °2-0.228 °2--0.4274 °2
S0.0035 Å °-0.0244 Å °-0.0631 Å °-0.0404 Å °-0.0301 Å °-0.0409 Å °0.0299 Å °0.081 Å °0.0126 Å °
Refinement TLS groupSelection details: all

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