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- PDB-1w87: FERREDOXIN-NADP REDUCTASE (MUTATION: Y 303 W) COMPLEXED WITH NADP... -

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Basic information

Entry
Database: PDB / ID: 1w87
TitleFERREDOXIN-NADP REDUCTASE (MUTATION: Y 303 W) COMPLEXED WITH NADP BY COCRYSTALLIZATION
ComponentsFERREDOXIN-NADP REDUCTASE
KeywordsOXIDOREDUCTASE / FAD / FLAVOPROTEIN / FNR / 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 / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHermoso, J.A. / Perez-Dorado, I. / Maya, 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: 2001
Title: Mechanism of Coenzyme Recognition and Binding Revealed by Crystal Structure Analysis of Ferredoxin-Nadp Reductase Complexed with Nadp
Authors: Hermoso, J.A. / Mayoral, T. / Faro, M. / Gomez-Moreno, C. / Sanz-Aparicio, J. / Medina, M.
History
DepositionSep 16, 2004Deposition 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: FERREDOXIN-NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4506
Polymers68,3922
Non-polymers3,0584
Water00
1
A: FERREDOXIN-NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7253
Polymers34,1961
Non-polymers1,5292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERREDOXIN-NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7253
Polymers34,1961
Non-polymers1,5292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)221.270, 221.270, 37.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95783, 0.02447, 0.28628), (-4.0E-5, -0.99638, 0.08502), (0.28732, 0.08142, 0.95437)
Vector: 278.49799, 134.60431, -47.30357)

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Components

#1: Protein FERREDOXIN-NADP REDUCTASE


Mass: 34195.910 Da / Num. of mol.: 2 / Fragment: RESIDUES 137-440 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Compound detailsCHAIN A, B ENGINEERED MUTATION TYR 440 TRP
Sequence detailsTYR 303 WAS MUTATED BY 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179
DetectorType: BRUKER-NONIUS / Detector: CCD / Date: Jul 7, 2004 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→34.99 Å / Num. obs: 16780 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 3.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.3 / % possible all: 48.2

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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: 3→34.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3233025.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ELECTRON DENSITY WAS NOT PRESENT FOR RESIDUES 0-8.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1159 6.9 %RANDOM
Rwork0.225 ---
obs0.225 16780 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2793 Å2 / ksol: 0.374794 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--16.69 Å20 Å20 Å2
2---16.69 Å20 Å2
3---33.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 202 0 4882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
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: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 135 7.1 %
Rwork0.382 1769 -
obs--60.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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