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- PDB-1gaq: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN FERREDOXIN AND FERREDOXI... -

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Basic information

Entry
Database: PDB / ID: 1gaq
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ REDUCTASE
Components
  • FERREDOXIN I
  • FERREDOXIN-NADP+ REDUCTASEFerredoxin—NADP(+) reductase
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


chloroplast thylakoid membrane protein complex / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / electron transport chain / response to light stimulus / photosynthesis / chloroplast ...chloroplast thylakoid membrane protein complex / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / electron transport chain / response to light stimulus / photosynthesis / chloroplast / 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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 / 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 / Resolution: 2.59 Å
AuthorsKurisu, G. / Kusunoki, M. / Hase, T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP(+) reductase.
Authors: Kurisu, G. / Kusunoki, M. / Katoh, E. / Yamazaki, T. / Teshima, K. / Onda, Y. / Kimata-Ariga, Y. / Hase, T.
History
DepositionMay 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 I
C: FERREDOXIN-NADP+ REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9866
Polymers81,2393
Non-polymers1,7473
Water2,396133
1
A: FERREDOXIN-NADP+ REDUCTASE
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8404
Polymers45,8792
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: FERREDOXIN-NADP+ REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1462
Polymers35,3601
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 93.410, 135.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FERREDOXIN-NADP+ REDUCTASE / Ferredoxin—NADP(+) reductase / FNR


Mass: 35360.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLP6, ferredoxin-NADP+ reductase
#2: Protein FERREDOXIN I / / FD


Mass: 10518.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P27787
#3: 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
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Tris, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
220 %(w/v)PEG40001reservoir
3100 mM1reservoirNaCl
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 33.9 Å2
Reflection shellResolution: 2.68→2.85 Å
Reflection
*PLUS
Highest resolution: 2.59 Å / Num. obs: 23300 / % possible obs: 97.8 % / Num. measured all: 319768 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 2.68 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.255

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.59→39.56 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1246520.54 / Data cutoff high rms absF: 3042258.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1152 5.1 %RANDOM
Rwork0.232 ---
obs-22761 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.4663 Å2 / ksol: 0.299211 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å20 Å2
2--4.23 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.59→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 110 133 5685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 2.59→2.75 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 181 4.9 %
Rwork0.318 3482 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.318

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