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- PDB-3w5u: Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase -

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Basic information

Entry
Database: PDB / ID: 3w5u
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. / Flavoprotein pyridine nucleotide cytochrome reductase / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 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: 2.7 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.ptnr2_label_atom_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

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Assembly

Deposited unit
A: Ferredoxin
B: Ferredoxin-1, chloroplastic
C: Ferredoxin
D: Ferredoxin-1, chloroplastic
E: Ferredoxin
F: Ferredoxin-1, chloroplastic
G: Ferredoxin
H: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,32116
Polymers183,4768
Non-polymers3,8458
Water59433
1
A: Ferredoxin
B: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8304
Polymers45,8692
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ferredoxin
D: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8304
Polymers45,8692
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ferredoxin
F: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8304
Polymers45,8692
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ferredoxin
H: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8304
Polymers45,8692
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.202, 153.634, 100.107
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.846914, 0.021869, 0.53128), (0.03133, -0.995366, 0.090915), (0.530806, 0.093642, 0.842304)-16.26394, -40.77868, 7.00941
3given(-0.970948, -0.015696, 0.238776), (-0.038315, 0.99517, -0.090384), (-0.236204, -0.096906, -0.966859)-8.32216, -0.36227, 56.51237
4given(0.687998, 0.005772, -0.72569), (0.009042, -0.999959, 0.000619), (-0.725656, -0.006987, -0.688022)21.36376, -35.41263, 49.19134

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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.: 4 / 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: 10534.435 Da / Num. of mol.: 4 / Fragment: UNP residues 53-150 / Mutation: S59C
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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 6000, 50mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.68→150 Å / Num. obs: 48206

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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: 2.7→45.46 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.839 / SU B: 13.835 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27975 2394 5 %RANDOM
Rwork0.22631 ---
obs0.22902 45176 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.921 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å2-0 Å2-1.26 Å2
2---3.1 Å2-0 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12224 0 228 33 12485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.98817247
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.73251549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16625.282568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.973152210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9271548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21842
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219564
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: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 171 -
Rwork0.268 3110 -
obs--93.8 %

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