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- PDB-1frn: THE INVOLVEMENT OF SER96 IN THE CATALYTIC MECHANISM OF FERREDOXIN... -

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Basic information

Entry
Database: PDB / ID: 1frn
TitleTHE INVOLVEMENT OF SER96 IN THE CATALYTIC MECHANISM OF FERREDOXIN-NADP+ REDUCTASE: STRUCTURE-FUNCTION RELATIONSHIP AS STUDIED BY SITE-DIRECTED MUTAGENESIS AND X-RAY CRYSTALLOGRAPHY
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 / NADPH dehydrogenase activity / chloroplast stroma / photosynthesis / electron transport chain
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 / PHOSPHATE ION / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBruns, C.M. / Karplus, P.A.
Citation
Journal: Biochemistry / Year: 1995
Title: Involvement of serine 96 in the catalytic mechanism of ferredoxin-NADP+ reductase: structure--function relationship as studied by site-directed mutagenesis and X-ray crystallography.
Authors: Aliverti, A. / Bruns, C.M. / Pandini, V.E. / Karplus, P.A. / Vanoni, M.A. / Curti, B. / Zanetti, G.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Refined Crystal Structure of Spinach Ferredoxin Reductase at 1.7 Angstroms Resolution: Oxidized, Reduced, and 2'-Phospho-5'-AMP Bound States
Authors: Bruns, C.M. / Karplus, P.A.
#2: 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
DepositionMar 31, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: FERREDOXIN-NADP+ REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4184
Polymers35,4421
Non-polymers9773
Water3,981221
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
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein FERREDOXIN-NADP+ REDUCTASE


Mass: 35441.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Organ: LEAF / Plasmid: PDS12/RBSII SPH(I) / Production host: Escherichia coli (E. coli) / References: UniProt: P00455, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND PH 4.6, RESIDUE 96 MUTATED FROM SERINE TO VALINE, RECOMBINANT VARIANT WITH PHENYLALANINE AT ...COMPND PH 4.6, RESIDUE 96 MUTATED FROM SERINE TO VALINE, RECOMBINANT VARIANT WITH PHENYLALANINE AT RESIDUE 269.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium acetate11
21.55-1.60 Mammonium sulfate11
33.4 mg/mlprotein11

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Data collection

Diffraction sourceWavelength: 1.5
DetectorType: SDMS / Date: Jun 15, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Num. obs: 22757 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
TNT5Arefinement
SDMSdata reduction
RefinementHighest resolution: 2 Å / σ(F): 0 /
RfactorNum. reflection
obs0.162 22757
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 63 221 2641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.4
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

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