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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 / homologyFlavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / 2Fe-2S ferredoxin-like superfamily / Beta-grasp domain superfamily / Ferredoxin [2Fe-2S], plant / Riboflavin synthase-like beta-barrel / 2Fe-2S ferredoxin, iron-sulphur binding site / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin--NADP reductase, plant and Cyanobacteria type ...Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / 2Fe-2S ferredoxin-like superfamily / Beta-grasp domain superfamily / Ferredoxin [2Fe-2S], plant / Riboflavin synthase-like beta-barrel / 2Fe-2S ferredoxin, iron-sulphur binding site / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / FAD-binding domain, ferredoxin reductase-type / 2Fe-2S iron-sulfur cluster binding domain / Oxidoreductase NAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Ferredoxin reductase-type FAD binding domain profile. / Ferredoxin--NADP reductase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / electron transport chain / chloroplast stroma / response to light stimulus / photosynthesis / 2 iron, 2 sulfur cluster binding / chloroplast / electron transfer activity / nucleotide binding / metal ion binding / Ferredoxin-1, chloroplastic / Ferredoxin--NADP reductase, chloroplastic
Function and homology information
Specimen sourceZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.59 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 8, 2000 / Release: Feb 7, 2001
RevisionDateData content typeGroupProviderType
1.0Feb 7, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers81,2393
Non-polymers1,7473
Water2,396133
1
A: FERREDOXIN-NADP+ REDUCTASE
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8404
Polyers45,8792
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
Polyers35,3601
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21

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Components

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


Mass: 35360.449 Da / Num. of mol.: 2 / Source: (gene. exp.) Zea mays (maize) / Genus: Zea / Plasmid name: PQE60 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLP6, ferredoxin-NADP+ reductase
#2: Protein/peptide FERREDOXIN I / / FD


Mass: 10518.369 Da / Num. of mol.: 1 / Source: (gene. exp.) Zea mays (maize) / Genus: Zea / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P27787
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


Mass: 18.015 Da / Num. of mol.: 133 / Formula: H2O / Water

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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 / Density percent sol: 44.71 %
Crystal growTemp: 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
Temp: 4 ℃
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Dec 18, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 33.9 Å2
Reflection shellHighest resolution: 2.68 Å / Lowest resolution: 2.85 Å
Reflection
*PLUS
D resolution high: 2.59 Å / Number obs: 23300 / Number measured all: 319768 / Percent possible obs: 97.8 / Rmerge I obs: 0.098
Reflection shell
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 2.68 Å / Percent possible obs: 96.6 / Rmerge I obs: 0.255

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.0refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineR Free selection details: RANDOM / 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 / Sigma F: 2
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 30.4663 / Solvent model param ksol: 0.299211
Displacement parametersB iso mean: 47.1 Å2 / Aniso B11: -4.4 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 4.23 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.17 Å2
Least-squares processR factor R free: 0.297 / R factor R free error: 0.009 / R factor R work: 0.232 / Highest resolution: 2.59 Å / Lowest resolution: 39.56 Å / Number reflection R free: 1152 / Number reflection obs: 22761 / Percent reflection R free: 5.1 / Percent reflection obs: 97.8
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.48 Å / Luzzati sigma a obs: 0.33 Å
Refine hist #LASTHighest resolution: 2.59 Å / Lowest resolution: 39.56 Å
Number of atoms included #LASTProtein: 5442 / Nucleic acid: 0 / Ligand: 110 / Solvent: 133 / Total: 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_it1.361.50
X-RAY DIFFRACTIONc_mcangle_it2.312.00
X-RAY DIFFRACTIONc_scbond_it1.812.00
X-RAY DIFFRACTIONc_scangle_it2.592.50
Refine LS shellHighest resolution: 2.59 Å / R factor R free: 0.4 / R factor R free error: 0.03 / R factor R work: 0.318 / Lowest resolution: 2.75 Å / Number reflection R free: 181 / Number reflection R work: 3482 / Total number of bins used: 6 / Percent reflection R free: 4.9 / Percent reflection 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
Refine
*PLUS
Sigma F: 2
Displacement parameters
*PLUS
B iso mean: 47.1 Å2
Least-squares process
*PLUS
R factor obs: 0.233 / Percent reflection R free: 5.1
Refine LS restraints
*PLUS
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.30
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.80
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.500
X-RAY DIFFRACTIONc_scbond_it2.000
X-RAY DIFFRACTIONc_mcangle_it2.000
X-RAY DIFFRACTIONc_scangle_it2.500
Refine LS shell
*PLUS
Percent reflection R free: 4.9 / R factor R free: 0.4 / R factor R work: 0.318

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