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- PDB-1bjk: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH ARG 264 REPLACED BY GLU (R264E) -

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Basic information

Entry
Database: PDB / ID: 1bjk
TitleFERREDOXIN:NADP+ REDUCTASE MUTANT WITH ARG 264 REPLACED BY GLU (R264E)
ComponentsFERREDOXIN--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 / flavin adenine dinucleotide binding / NADP 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 / 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 / CpcD-like domain / Ferredoxin--NADP reductase / 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. / Martinez-Ripoll, M. / Martinez-Julvez, M. / Sanz-Aparicio, J. / Gomez-Moreno, C.
Citation
Journal: Biochemistry / Year: 1998
Title: Role of Arg100 and Arg264 from Anabaena PCC 7119 ferredoxin-NADP+ reductase for optimal NADP+ binding and electron transfer.
Authors: Martinez-Julvez, M. / Hermoso, J. / Hurley, J.K. / Mayoral, T. / Sanz-Aparicio, J. / Tollin, G. / Gomez-Moreno, C. / Medina, M.
#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
DepositionJun 25, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)34,0563
Polymers33,1751
Non-polymers8822
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.090, 88.090, 97.210
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 FERREDOXIN--NADP+ REDUCTASE / FNR


Mass: 33174.625 Da / Num. of mol.: 1 / Mutation: R264E
Source method: isolated from a genetically manipulated source
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.: 332 / 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 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.3 mg/mlprotein1drop
24 mMTris-HCl1drop
31 %(w/v)beta-octylglucoside1drop
410.8 %(w/v)PEG60001drop
58 mMammonium sulfate1drop
60.04 MMES1drop
717 %(w/v)PEG60001reservoir
820 mMammonium sulfate1reservoir
90.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.58 Å / Num. obs: 18847 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 6.1
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.4 / % possible all: 94.4

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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→9 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1295 7 %RANDOM
Rwork0.166 ---
obs0.166 18504 91.7 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 58 332 2726
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_deg1.21
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.17
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 -12.5 %
Rwork0.227 159 -
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55
LS refinement shell
*PLUS
Rfactor Rfree: 0.27

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