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- PDB-1qfz: PEA FNR Y308S MUTANT IN COMPLEX WITH NADPH -

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Basic information

Entry
Database: PDB / ID: 1qfz
TitlePEA FNR Y308S MUTANT IN COMPLEX WITH NADPH
ComponentsPROTEIN (FERREDOXIN:NADP+ REDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / PHOTOSYNTHESIS / ELECTRON TRANSFER / HYDRIDE TRANSFER
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / chloroplast stroma / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / 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--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / 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 / Chem-NDP / Ferredoxin--NADP reductase, leaf isozyme, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDeng, Z. / Aliverti, A. / Zanetti, G. / Arakaki, A.K. / Ottado, J. / Orellano, E.G. / Calcaterra, N.B. / Ceccarelli, E.A. / Carrillo, N. / Karplus, P.A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: A productive NADP+ binding mode of ferredoxin-NADP+ reductase revealed by protein engineering and crystallographic studies.
Authors: Deng, Z. / Aliverti, A. / Zanetti, G. / Arakaki, A.K. / Ottado, J. / Orellano, E.G. / Calcaterra, N.B. / Ceccarelli, E.A. / Carrillo, N. / Karplus, P.A.
History
DepositionApr 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,6947
Polymers69,5362
Non-polymers3,1585
Water13,367742
1
A: PROTEIN (FERREDOXIN:NADP+ REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3954
Polymers34,7681
Non-polymers1,6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FERREDOXIN:NADP+ REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2993
Polymers34,7681
Non-polymers1,5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.360, 110.090, 80.920
Angle α, β, γ (deg.)90.00, 93.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.986029, -0.044485, -0.160521), (-0.038152, 0.998375, -0.042323), (0.162143, -0.035608, -0.986125)
Vector: 22.6832, 3.4431, 40.5246)

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Components

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


Mass: 34767.969 Da / Num. of mol.: 2 / Mutation: Y308S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Organ: LEAF / Production host: Escherichia coli (E. coli) / References: UniProt: P10933, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
25 mMpotassium phosphate1drop
32.1 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorDetector: CCD / Date: Feb 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 92562 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rsym value: 0.052 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.279 / % possible all: 90.6
Reflection
*PLUS
Num. measured all: 357117 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 90.6 % / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.8refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Y308S:NADP+

Resolution: 1.7→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4646 5 %RANDOM
Rwork0.201 ---
obs-91340 95.6 %-
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-10.07 Å20 Å21.079 Å2
2---6.18 Å20 Å2
3----3.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 207 742 5729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 512 5 %
Rwork0.359 6294 -
obs--89.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.37 / % reflection Rfree: 5 % / Rfactor Rwork: 0.359

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