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- PDB-1w35: FERREDOXIN-NADP+ REDUCTASE (MUTATION: Y 303 W) -

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Basic information

Entry
Database: PDB / ID: 1w35
TitleFERREDOXIN-NADP+ REDUCTASE (MUTATION: Y 303 W)
ComponentsFERREDOXIN-NADP+ REDUCTASEFerredoxin—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 / 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 speciesANABAENA PCC7119 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHermoso, J.A. / Perez-Dorado, I. / Medina, M. / Julvez, M.M. / Sanz-Aparicio, J. / Gomez-Moreno, C.
Citation
Journal: 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. / Julvez, M.M. / Sanz-Aparicio, J. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: X-Ray Structure of the Ferredoxin:Nadp+ Reductase from the Cyanobacterium Anabanena Pcc 7119 at 1.8 Angstroms Resolution, and Crystallographic Studies of Nadp+ Binding at 2.25 Angstroms Resolution
Authors: Serre, L. / Vellieux, F.M. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M.
History
DepositionJul 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 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

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Assembly

Deposited unit
A: FERREDOXIN-NADP+ REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0783
Polymers34,1961
Non-polymers8822
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.085, 87.085, 96.231
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 / Ferredoxin—NADP(+) reductase / FNR


Mass: 34195.910 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-440 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA PCC7119 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAIN A TYR 303 TRP

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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 5.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179
DetectorDetector: CCD / Date: Jul 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.902→32.285 Å / Num. obs: 32488 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

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

1gjr


Resolution: 1.9→32.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1896636.97 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: ELECTRON DENSITY WAS NOT PRESENT FOR RESIDUES 0-8.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2269 7 %RANDOM
Rwork0.171 ---
obs0.171 32488 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6573 Å2 / ksol: 0.409845 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20.58 Å20 Å2
2--2.82 Å20 Å2
3----5.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 58 492 2889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.29
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: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 364 6.9 %
Rwork0.196 4901 -
obs--97.2 %

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