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- PDB-5vw3: NADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductase -

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Basic information

Entry
Database: PDB / ID: 5vw3
TitleNADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductase
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / NADPH binding / photosynthesis / electron transport chain / electron transfer activity / nucleotide binding
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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.453 Å
AuthorsKean, K.M. / Carpenter, R.A. / Hall, A.R. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM119227 United States
National Science Foundation (NSF, United States)MCB-9982727 United States
CitationJournal: FEBS J. / Year: 2017
Title: High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily.
Authors: Kean, K.M. / Carpenter, R.A. / Pandini, V. / Zanetti, G. / Hall, A.R. / Faber, R. / Aliverti, A. / Karplus, P.A.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,8985
Polymers35,2861
Non-polymers1,6124
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.813, 58.813, 187.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-245-

GLY

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferredoxin--NADP reductase


Mass: 35285.902 Da / Num. of mol.: 1 / Mutation: Y316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase

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Non-polymers , 5 types, 495 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: 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
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22-24% PEG 8000, 0.1 M sodium cacodylate (pH 6-7), 0.18-0.22 M magnesium acetate, 100 mM nicotinamide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50.93 Å / Num. obs: 65831 / % possible obs: 97.9 % / Redundancy: 9.6 % / Net I/σ(I): 14.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 8739 / Rpim(I) all: 0.024 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LO8

3lo8


Resolution: 1.453→50.93 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.1
Details: Atoms C5D, C4D, O4D, C3D, O3D, C2D, O2D, N1N, and C1D of NAP modeled as 0.60 (A) and 0.40 (B) occupancy where alternate conformation is visible. All other atoms modeled as 1.0 (A) and 0.0 (B) ...Details: Atoms C5D, C4D, O4D, C3D, O3D, C2D, O2D, N1N, and C1D of NAP modeled as 0.60 (A) and 0.40 (B) occupancy where alternate conformation is visible. All other atoms modeled as 1.0 (A) and 0.0 (B) to reflect only one visible conformation for the remainder of NAP.
RfactorNum. reflection% reflection
Rfree0.1435 6645 10.11 %
Rwork0.1077 --
obs0.1113 65751 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.453→50.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 106 491 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082766
X-RAY DIFFRACTIONf_angle_d1.2093813
X-RAY DIFFRACTIONf_dihedral_angle_d18.8831075
X-RAY DIFFRACTIONf_chiral_restr0.079397
X-RAY DIFFRACTIONf_plane_restr0.006486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4531-1.46960.19292260.14351707X-RAY DIFFRACTION87
1.4696-1.48690.19342240.13681730X-RAY DIFFRACTION90
1.4869-1.5050.18362170.1321856X-RAY DIFFRACTION91
1.505-1.52410.18311830.12071801X-RAY DIFFRACTION91
1.5241-1.54410.16321830.11011853X-RAY DIFFRACTION91
1.5441-1.56530.16472000.1121803X-RAY DIFFRACTION92
1.5653-1.58760.16242040.11771927X-RAY DIFFRACTION94
1.5876-1.61130.16982100.10991891X-RAY DIFFRACTION97
1.6113-1.63650.16572140.1061999X-RAY DIFFRACTION98
1.6365-1.66330.1542190.09851937X-RAY DIFFRACTION98
1.6633-1.6920.17052090.09791994X-RAY DIFFRACTION98
1.692-1.72280.14522400.08881944X-RAY DIFFRACTION99
1.7228-1.75590.13292380.09181943X-RAY DIFFRACTION99
1.7559-1.79180.15722360.09331985X-RAY DIFFRACTION99
1.7918-1.83070.13582560.08961958X-RAY DIFFRACTION100
1.8307-1.87330.13532300.09471997X-RAY DIFFRACTION100
1.8733-1.92020.12162110.0922016X-RAY DIFFRACTION100
1.9202-1.97210.12692220.08652015X-RAY DIFFRACTION100
1.9721-2.03010.12322110.08322053X-RAY DIFFRACTION100
2.0301-2.09570.12632260.0852000X-RAY DIFFRACTION100
2.0957-2.17060.12152530.08591994X-RAY DIFFRACTION100
2.1706-2.25750.1332180.08722050X-RAY DIFFRACTION100
2.2575-2.36020.14372170.09662020X-RAY DIFFRACTION100
2.3602-2.48460.13772190.09622037X-RAY DIFFRACTION100
2.4846-2.64030.14522000.09562065X-RAY DIFFRACTION100
2.6403-2.84410.12952300.10182049X-RAY DIFFRACTION100
2.8441-3.13030.14722330.10822056X-RAY DIFFRACTION100
3.1303-3.58320.12892390.1042058X-RAY DIFFRACTION100
3.5832-4.5140.11932280.11082136X-RAY DIFFRACTION100
4.514-50.96510.18962490.17652232X-RAY DIFFRACTION100

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