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- PDB-1ewy: ANABAENA PCC7119 FERREDOXIN:FERREDOXIN-NADP+-REDUCTASE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ewy
TitleANABAENA PCC7119 FERREDOXIN:FERREDOXIN-NADP+-REDUCTASE COMPLEX
Components
  • FERREDOXIN I
  • FERREDOXIN-NADP REDUCTASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER COMPLEX / PHOTOSYNTHESIS / PROTEIN-PROTEIN INTERACTION / FERREDOXIN / REDUCTASE
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / 2 iron, 2 sulfur cluster binding / NADP binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / CpcD-like domain / Ferredoxin--NADP reductase / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / 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. ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / CpcD-like domain / Ferredoxin--NADP reductase / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / 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. / Beta-grasp domain / 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 / 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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesNostoc sp. PCC 7119 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsMorales, R. / Charon, M.H. / Frey, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule.
Authors: Morales, R. / Kachalova, G. / Vellieux, F. / Charon, M.H. / Frey, M.
#1: Journal: Embo J. / Year: 2000
Title: A Redox-Dependent Interaction between Two Electron-Transfer Partners Involved in Photosynthesis
Authors: Morales, R. / Charon, M.H. / Kachalova, G. / Serre, L.S. / Medina, M. / Gomez-Moreno, C. / Frey, M.
History
DepositionApr 28, 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 1.3Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300The biological molecule consists of one ferredoxin-NADP reductase and one ferredoxin I. Biomolecule ...The biological molecule consists of one ferredoxin-NADP reductase and one ferredoxin I. Biomolecule 2 in REMARK 350 is meaningless.

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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-NADP REDUCTASE
C: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5386
Polymers78,7913
Non-polymers1,7473
Water1,60389
1
A: FERREDOXIN-NADP REDUCTASE
C: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7104
Polymers44,7482
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN-NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8282
Polymers34,0431
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.730, 63.720, 158.020
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


Mass: 34042.660 Da / Num. of mol.: 2 / Fragment: 138-440 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7119 (bacteria) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Protein FERREDOXIN I


Mass: 10705.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7119 (bacteria) / References: UniProt: P0A3C8
#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.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.73 Å3/Da / Density % sol: 28.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20-24% PEG 6000,10 mM MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.7 mMoxidized FNR1drop
20.5 mMoxidized Fd1drop
30.1 MTris-HCl1droppH8.0
45 %beta-octylglucoside1drop
50.1 MMES1reservoirpH5.5
618-21 %(w/v)PEG60001reservoir
70.1 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. all: 175226 / Num. obs: 25838 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 7.9
Reflection shellResolution: 2.28→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2586 / % possible all: 87.7
Reflection
*PLUS
Num. measured all: 175226 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 87.7 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 7.3

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QUE FOR FERREDOXIN-NADP+REDUCTASE

1que


Resolution: 2.38→15 Å / Num. parameters: 22871 / Num. restraintsaints: 23488 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: The Twin option in SHELX97 was used, with the TWIN 0 1 0 1 0 0 0 0 -1 2 command.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2563 10 %RANDOM
Rwork0.2188 ---
all0.2317 25701 --
obs0.2317 23138 87.6 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5503
Refinement stepCycle: LAST / Resolution: 2.38→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 110 89 5722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.001
X-RAY DIFFRACTIONs_angle_d0.002
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0329
X-RAY DIFFRACTIONs_zero_chiral_vol0.003
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.004
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.098
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor all: 0.232 / Rfactor obs: 0.219 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_plane_restr0.033
X-RAY DIFFRACTIONs_chiral_restr0.003

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