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- PDB-9l8g: R115A mutant of Ferredoxin-NADP+ reductase from maize root - Oxid... -

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Basic information

Entry
Database: PDB / ID: 9l8g
TitleR115A mutant of Ferredoxin-NADP+ reductase from maize root - Oxidized form, low X-ray dose
ComponentsFerredoxin--NADP reductase, chloroplastic
KeywordsOXIDOREDUCTASE / electron transfer / Flavoprotein
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / photosynthesis / chloroplast / nucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsUenaka, M. / Ohnishi, Y. / Tanaka, H. / Kurisu, G.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJSP2138 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP + reductase revealed by high-resolution X-ray and neutron crystallography.
Authors: Uenaka, M. / Ohnishi, Y. / Ise, A. / Yu, J. / Yano, N. / Kusaka, K. / Tanaka, H. / Kurisu, G.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6944
Polymers34,5181
Non-polymers1,1763
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-2 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.170, 59.170, 186.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Ferredoxin--NADP reductase, chloroplastic / FNR


Mass: 34518.074 Da / Num. of mol.: 1 / Fragment: UNP residues 17-327 / Mutation: R115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 542713, ZEAMMB73_Zm00001d034345 / Production host: Escherichia coli (E. coli) / References: UniProt: B4G043, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293.15 K / Method: batch mode / Details: PEG2000 29.5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→49.41 Å / Num. obs: 83861 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.9
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4086 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H59

5h59


Resolution: 1.35→49.41 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 4193 5 %
Rwork0.1726 79663 -
obs0.1733 83856 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.71 Å2
Refinement stepCycle: LAST / Resolution: 1.35→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 77 437 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712846
X-RAY DIFFRACTIONf_angle_d0.98423886
X-RAY DIFFRACTIONf_chiral_restr0.0897391
X-RAY DIFFRACTIONf_plane_restr0.0086525
X-RAY DIFFRACTIONf_dihedral_angle_d12.1565459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.31571540.30582590X-RAY DIFFRACTION99.85
1.37-1.380.32071250.30062641X-RAY DIFFRACTION99.78
1.38-1.40.2881320.26682623X-RAY DIFFRACTION99.96
1.4-1.420.27171370.26242625X-RAY DIFFRACTION100
1.42-1.430.26131460.24792605X-RAY DIFFRACTION100
1.43-1.450.28341250.24042635X-RAY DIFFRACTION99.89
1.45-1.480.21231350.22992655X-RAY DIFFRACTION99.89
1.48-1.50.21771030.22112625X-RAY DIFFRACTION99.89
1.5-1.520.24531480.21172673X-RAY DIFFRACTION99.96
1.52-1.550.23761310.20632615X-RAY DIFFRACTION100
1.55-1.570.22771450.20422615X-RAY DIFFRACTION99.82
1.57-1.60.20351380.2062673X-RAY DIFFRACTION99.82
1.6-1.630.20071220.20012610X-RAY DIFFRACTION100
1.63-1.660.2181320.19422658X-RAY DIFFRACTION99.93
1.66-1.70.20481470.19022651X-RAY DIFFRACTION99.96
1.7-1.740.19251490.17722646X-RAY DIFFRACTION99.96
1.74-1.780.19131590.18092598X-RAY DIFFRACTION100
1.78-1.830.16481560.17272647X-RAY DIFFRACTION100
1.83-1.890.19431710.16432621X-RAY DIFFRACTION100
1.89-1.950.16461210.162659X-RAY DIFFRACTION99.86
1.95-2.020.17671110.16312686X-RAY DIFFRACTION99.82
2.02-2.10.19421390.16512675X-RAY DIFFRACTION99.79
2.1-2.190.17531450.16072686X-RAY DIFFRACTION99.93
2.19-2.310.18041240.16182656X-RAY DIFFRACTION99.78
2.31-2.450.18811740.16732657X-RAY DIFFRACTION99.02
2.45-2.640.17741440.16122635X-RAY DIFFRACTION98.62
2.64-2.910.19871540.16592673X-RAY DIFFRACTION99.3
2.91-3.330.171600.15392713X-RAY DIFFRACTION99.31
3.33-4.190.13051460.13562733X-RAY DIFFRACTION99
4.19-49.410.19481200.16642884X-RAY DIFFRACTION97.25

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