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- PDB-2bsa: Ferredoxin-Nadp Reductase (Mutation: Y 303 S) complexed with NADP -

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Basic information

Entry
Database: PDB / ID: 2bsa
TitleFerredoxin-Nadp Reductase (Mutation: Y 303 S) complexed with NADP
ComponentsFERREDOXIN-NADP REDUCTASE
KeywordsOXIDOREDUCTASE / FAD / FLAVOPROTEIN / FNR / MEMBRANE / NADP / NADP REDUCTASE / PHYCOBILISOME / THYLAKOID
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMaya, C.M. / Hermoso, J.A. / Perez-Dorado, I. / Tejero, J. / Julvez, M.M. / Gomez-Moreno, C. / Medina, M.
CitationJournal: Biochemistry / Year: 2005
Title: C-Terminal Tyrosine of Ferredoxin-Nadp(+) Reductase in Hydride Transfer Processes with Nad(P)(+)/H.
Authors: Tejero, J. / Perez-Dorado, I. / Maya, C.M. / Julvez, M.M. / Sanz-Aparicio, J. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M.
History
DepositionMay 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)35,4363
Polymers33,9081
Non-polymers1,5292
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.154, 87.154, 96.815
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: 33907.543 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC7119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: REDUCED FERREDOXIN + NADP(+) = OXIDIZED FERREDOXIN + NADPH ENGINEERED RESIDUE ...CATALYTIC ACTIVITY: REDUCED FERREDOXIN + NADP(+) = OXIDIZED FERREDOXIN + NADPH ENGINEERED RESIDUE IN CHAIN A, TYR 440 TO SER

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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: 59 %
Crystal growpH: 5.5 / Details: pH 5.50

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2004 / Details: MIRRORS
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→27.32 Å / Num. obs: 31825 / % possible obs: 99.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 8.6 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GJR

1gjr


Resolution: 1.92→27.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1732632.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2229 7 %RANDOM
Rwork0.197 ---
obs0.197 31825 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.293 Å2 / ksol: 0.405993 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å22.19 Å20 Å2
2--1.95 Å20 Å2
3----3.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.92→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 101 279 2708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.92→2.04 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 384 7.2 %
Rwork0.199 4919 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FAD.PARFAD.TOP
X-RAY DIFFRACTION4NAP.PARNAP-Z.TOP

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