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- PDB-5h5j: Complex between ferredoxin and ferredoxin-NADP+ reductase from ma... -

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Basic information

Entry
Database: PDB / ID: 5h5j
TitleComplex between ferredoxin and ferredoxin-NADP+ reductase from maize root
Components
  • Ferredoxin--NADP reductase
  • Ferredoxin-3, chloroplastic
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Electron transfer complex / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


etioplast stroma / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / NADPH binding / photosynthesis / chloroplast / electron transport chain ...etioplast stroma / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / NADPH binding / photosynthesis / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Ferredoxin [2Fe-2S], plant / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Ferredoxin [2Fe-2S], plant / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / 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 / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin--NADP reductase, chloroplastic / Ferredoxin-3, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKurisu, G. / Hase, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST-CREST Japan
Citation
Journal: Photosyn. Res. / Year: 2017
Title: Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP(+) oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation
Authors: Shinohara, F. / Kurisu, G. / Hanke, G. / Bowsher, C. / Hase, T. / Kimata-Ariga, Y.
#1: Journal: Photosyn. Res. / Year: 2004
Title: Fd : FNR Electron Transfer Complexes: Evolutionary Refinement of Structural Interactions
Authors: Hanke, G.T. / Kurisu, G. / Kusunoki, M. / Hase, T.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin-3, chloroplastic
C: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3746
Polymers79,6273
Non-polymers1,7473
Water6,017334
1
A: Ferredoxin--NADP reductase
B: Ferredoxin-3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9564
Polymers44,9942
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-27 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4182
Polymers34,6321
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.718, 126.576, 59.367
Angle α, β, γ (deg.)90.00, 114.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 34632.242 Da / Num. of mol.: 2 / Fragment: UNP residues 19-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase
#2: Protein Ferredoxin-3, chloroplastic / / Ferredoxin III / Fd III


Mass: 10362.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: FDX3, PFD3 / Production host: Escherichia coli (E. coli) / References: UniProt: P27788
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Fe2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20 % PEG6000, 100 mM Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 91157 / % possible obs: 99.4 % / Redundancy: 3.74 % / Biso Wilson estimate: 19.9 Å2 / Net I/σ(I): 25.7

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H59

5h59


Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4560843.87 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USE
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1217 5 %RANDOM
Rwork0.191 ---
obs0.191 24282 99.4 %-
Solvent computationBsol: 35.577 Å2 / ksol: 0.370307 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å23.08 Å2
2--4.78 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: 1 / Resolution: 2.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 110 334 6043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 199 5 %
Rwork0.231 3781 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fad.parfad.top
X-RAY DIFFRACTION4fes.parfes.top

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