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- PDB-1fnd: REFINED CRYSTAL STRUCTURE OF SPINACH FERREDOXIN REDUCTASE AT 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 1fnd
TitleREFINED CRYSTAL STRUCTURE OF SPINACH FERREDOXIN REDUCTASE AT 1.7 ANGSTROMS RESOLUTION: OXIDIZED, REDUCED, AND 2'-PHOSPHO-5'-AMP BOUND STATES
ComponentsFERREDOXIN-NADP+ REDUCTASE
KeywordsOXIDOREDUCTASE (NADP+(A) / FERREDOXIN(A))
Function / homology
Function and homology information


chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / chloroplast stroma / 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
ADENOSINE-2'-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBruns, C.M. / Karplus, P.A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states.
Authors: Bruns, C.M. / Karplus, P.A.
#1: Journal: Science / Year: 1991
Title: Atomic Structure of Ferredoxin-Nadp+ Reductase: Prototype for a Structurally Novel Flavoenzyme Family
Authors: Karplus, P.A. / Daniels, M.J. / Herriott, J.R.
History
DepositionJan 5, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
SupersessionMay 15, 1995ID: 2FNR
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)36,6914
Polymers35,3821
Non-polymers1,3093
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.700, 57.700, 68.100
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 150

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Components

#1: Protein FERREDOXIN-NADP+ REDUCTASE


Mass: 35381.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / References: UniProt: P00455, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growDetails: PH 4.6
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Mammonium sulfate1reservoir
20.2 MMcIlvain's buffer1reservoirsodium citrate-phosphate

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 37112 / % possible obs: 98 % / Redundancy: 2.6 % / Num. measured all: 95754 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: TNT / Version: 5A / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(I): 3
Details: DURING REFINEMENT, THE MAXIMUM TEMPERATURE FACTOR ALLOWED WAS 100.00.
RfactorNum. reflection
obs0.174 37112
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 90 216 2658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Lowest resolution: 9999 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2

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