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- PDB-1jb9: Crystal Structure of The Ferredoxin:NADP+ Reductase From Maize Ro... -

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Basic information

Entry
Database: PDB / ID: 1jb9
TitleCrystal Structure of The Ferredoxin:NADP+ Reductase From Maize Root AT 1.7 Angstroms
Componentsferredoxin-NADP reductaseFerredoxin—NADP(+) reductase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / NADPH binding / photosynthesis / electron transport chain / electron transfer activity
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / 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--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / 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 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFaber, H.R. / Karplus, P.A. / Aliverti, A. / Ferioli, C. / Spinola, M.
Citation
Journal: Biochemistry / Year: 2001
Title: Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues.
Authors: Aliverti, A. / Faber, R. / Finnerty, C.M. / Ferioli, C. / Pandini, V. / Negri, A. / Karplus, P.A. / Zanetti, G.
#1: Journal: FLAVINS AND FLAVOPROTEINS / Year: 1999
Title: Structural and Functional Properties of Corn Root Ferredoxin:NADP+ Reductase
Authors: Aliverti, A. / Ferioli, C. / Spinola, M. / Raimondi, D. / Zanetti, G. / Finnerty, C. / Faber, R. / Karplus, P.A.
History
DepositionJun 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 11, 2012Group: Database references
Revision 1.4Mar 26, 2014Group: Database references
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 1.6Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1482
Polymers35,3621
Non-polymers7861
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.670, 59.670, 189.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ferredoxin-NADP reductase / Ferredoxin—NADP(+) reductase


Mass: 35361.996 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: Q41736, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Peg 8000, Na Cacodylate, Mg Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
210 mMHEPES1droppH7.0
320 %PEG80001reservoir
40.1 Msodium cacodylate1reservoirpH6.5
50.2 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2000 / Details: Yale Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 47556 / Num. obs: 47556 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→50 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Num. obs: 43654 / % possible obs: 99.1 % / Num. measured all: 246386 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.364

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Processing

Software
NameClassification
SCALEPACKdata scaling
MRXmodel building
TNTrefinement
MRXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modified 1FNB

1fnb


Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4757 -Random
Rwork0.164 ---
all0.167 43687 --
obs0.167 43687 10 %-
Solvent computationBsol: 227.851 Å2 / ksol: 0.78246 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.17 Å21.17 Å20 Å2
2--1.17 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 53 276 2752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONt_angle_deg2.0670.93432
X-RAY DIFFRACTIONt_bond_d0.0131.72546
X-RAY DIFFRACTIONt_dihedral_angle_d17.9101481
X-RAY DIFFRACTIONt_trig_c_planes0.016262
X-RAY DIFFRACTIONt_gen_planes0.0195360
X-RAY DIFFRACTIONt_nbd0.0251015
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.167 / Rfactor obs: 0.164 / Rfactor Rfree: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d17.91
X-RAY DIFFRACTIONt_planar_d0.016
X-RAY DIFFRACTIONt_plane_restr0.019

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