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- PDB-1qgz: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 78 REPLACED BY ASP (L78D) -

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Basic information

Entry
Database: PDB / ID: 1qgz
TitleFERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 78 REPLACED BY ASP (L78D)
ComponentsPROTEIN (FERREDOXIN:NADP+ REDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / NADP REDUCTASE
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / 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 speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHermoso, J.A. / Mayoral, T. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Role of a cluster of hydrophobic residues near the FAD cofactor in Anabaena PCC 7119 ferredoxin-NADP+ reductase for optimal complex formation and electron transfer to ferredoxin.
Authors: Martinez-Julvez, M. / Nogues, I. / Faro, M. / Hurley, J.K. / Brodie, T.B. / Mayoral, T. / Sanz-Aparicio, J. / Hermoso, J.A. / Stankovich, M.T. / Medina, M. / Tollin, G. / Gomez-Moreno, C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution.
Authors: Serre, L. / Vellieux, F.M. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M.
History
DepositionMay 10, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 27, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: PROTEIN (FERREDOXIN:NADP+ REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0863
Polymers33,2051
Non-polymers8822
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.030, 88.030, 97.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTEIN (FERREDOXIN:NADP+ REDUCTASE) / FNR


Mass: 33204.637 Da / Num. of mol.: 1 / Mutation: L78D
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH FLAVIN-ADENINE DINUCLEOTIDE / Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Production host: Escherichia coli (E. coli) / References: UniProt: P21890, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.75 mMprotein1drop
210 mMTris-HCl1droppH8.0
35 %(w/v)beta-octylglucoside1dropunbuffered
418-20 %(w/v)PEG60001reservoir
520 mMammonium sulfate1reservoir
60.1 MMES- NaOH1reservoirpH5.0

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.57 Å / Num. obs: 18686 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.224 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 35.6 Å
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUE

1que


Resolution: 2.3→7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1305 7 %RANDOM
Rwork0.177 ---
obs-17976 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 58 268 2664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.19
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 -7 %
Rwork0.22 1759 -
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.178 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 7 % / Rfactor Rwork: 0.22

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