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- PDB-3w5v: Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase -

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Basic information

Entry
Database: PDB / ID: 3w5v
TitleCross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase
Components
  • Ferredoxin
  • Ferredoxin-1, chloroplastic
KeywordsELECTRON TRANSPORT / electron transfer complex
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / response to light stimulus / photosynthesis / chloroplast / electron transport chain ...oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / response to light stimulus / 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 / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Ferredoxin [2Fe-2S], plant / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / 2Fe-2S ferredoxin-like superfamily / 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 / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin-1, chloroplastic / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsKimata-Ariga, Y. / Kubota-Kawai, H. / Muraki, N. / Hase, T. / Kurisu, G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP(+) reductase
Authors: Kimata-Ariga, Y. / Kubota-Kawai, H. / Lee, Y.-H. / Muraki, N. / Ikegami, T. / Kurisu, G. / Hase, T.
History
DepositionFeb 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin
B: Ferredoxin-1, chloroplastic
C: Ferredoxin
D: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6938
Polymers91,7704
Non-polymers1,9234
Water00
1
A: Ferredoxin
D: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8464
Polymers45,8852
Non-polymers9612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-28 kcal/mol
Surface area19220 Å2
MethodPISA
2
B: Ferredoxin-1, chloroplastic
C: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8464
Polymers45,8852
Non-polymers9612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-28 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.170, 120.345, 84.577
Angle α, β, γ (deg.)90.00, 109.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.900585, -0.360692, 0.242586), (-0.323557, 0.183576, -0.92823), (0.290273, -0.91444, -0.28203)-93.40076, 33.0957, 74.35553

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Components

#1: Protein Ferredoxin / Ferredoxin--NADP reductase / leaf isozyme / FerredoxinFerredoxin--NADP reductase / leaf isozyme / ...Ferredoxin--NADP reductase / leaf isozyme / FerredoxinFerredoxin--NADP reductase / leaf isozyme / Uncharacterized protein


Mass: 35334.477 Da / Num. of mol.: 2 / Fragment: UNP residues 42-355 / Mutation: E19C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: L-FNRI, ZEAMMB73_343560 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLP6
#2: Protein Ferredoxin-1, chloroplastic / Ferredoxin I / Fd I


Mass: 10550.435 Da / Num. of mol.: 2 / Fragment: UNP residues 53-150 / Mutation: A70C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: FDX1, PFD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27787
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
Has protein modificationY

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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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 8000, 20% ethylene glycol, 100mM Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 13803

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAW, 3B2F

1gaw

3b2f


Resolution: 3.81→35.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 73.326 / SU ML: 0.92 / Cross valid method: THROUGHOUT / ESU R Free: 0.827 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30613 683 5 %RANDOM
Rwork0.27745 ---
obs0.27895 13076 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.07 Å2
2--0.12 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 3.81→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 114 0 6290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9898708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73925.315286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4281524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.808→3.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.65 51 -
Rwork0.587 878 -
obs--93.74 %

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