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- PDB-1qg0: WILD-TYPE PEA FNR -

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Basic information

Entry
Database: PDB / ID: 1qg0
TitleWILD-TYPE PEA FNR
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 / Ferredoxin--NADP reductase, leaf isozyme, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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)71,2594
Polymers69,6882
Non-polymers1,5712
Water3,783210
1
A: PROTEIN (FERREDOXIN:NADP+ REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6302
Polymers34,8441
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FERREDOXIN:NADP+ REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6302
Polymers34,8441
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.900, 94.100, 140.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.09991, -0.992008, -0.077065), (-0.994929, 0.098702, 0.019336), (-0.011575, 0.078606, -0.996839)
Vector: 76.0604, 63.0563, 164.9767)

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Components

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


Mass: 34844.062 Da / Num. of mol.: 2
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.2 / Details: pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 33119 / % possible obs: 93.5 % / Redundancy: 5.6 % / Rsym value: 0.072 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.293 / % possible all: 76.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1FNB

1fnb


Resolution: 2.5→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1664 5 %RANDOM
Rwork0.218 ---
obs-27961 83.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.523 Å20 Å20 Å2
2--13.96 Å20 Å2
3----15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 106 210 5030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.7
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: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4066 125 5 %
Rwork0.3725 2094 -
obs--53.9 %

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