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- PDB-9kk7: Neutron structure of Ferredoxin-NADP+ reductase from maize root -... -

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Basic information

Entry
Database: PDB / ID: 9kk7
TitleNeutron structure of Ferredoxin-NADP+ reductase from maize root -Reduced form
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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionNov 13, 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
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,7824
Polymers34,6041
Non-polymers1,1783
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-4 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.32, 59.32, 187.69
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 34604.191 Da / Num. of mol.: 1 / Fragment: UNP residues 17-327
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293.15 K / Method: batch mode / Details: PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 2.05-5.38
DetectorType: iBIX / Detector: DIFFRACTOMETER / Date: Dec 10, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.051
25.381
ReflectionResolution: 1.8→19.425 Å / Num. obs: 36398 / % possible obs: 99.9 % / Redundancy: 9.5293 % / CC1/2: 0.9613 / Rpim(I) all: 0.1669 / Net I/σ(I): 5.41
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3565 / CC1/2: 0.3668 / Rpim(I) all: 0.7279

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Processing

Software
NameVersionClassification
STARGazerdata reduction
STARGazerdata scaling
PHASERphasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H59

5h59


Resolution: 1.8→19.425 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.208 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.161
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2462 1771 4.866 %
Rwork0.1971 34626 -
all0.199 --
obs-36397 99.66 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.027 Å2-0.014 Å2-0 Å2
2---0.027 Å2-0 Å2
3---0.089 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
NEUTRON DIFFRACTIONr_bond_refined_d0.0090.0144090
NEUTRON DIFFRACTIONr_bond_other_d0.0010.0171935
NEUTRON DIFFRACTIONr_ext_dist_refined_b00.0077866
NEUTRON DIFFRACTIONr_angle_refined_deg1.7832.0085103
NEUTRON DIFFRACTIONr_angle_other_deg0.6031.7074712
NEUTRON DIFFRACTIONr_dihedral_angle_1_deg6.3445324
NEUTRON DIFFRACTIONr_dihedral_angle_2_deg7.01310993.95691
NEUTRON DIFFRACTIONr_dihedral_angle_3_deg15.510510
NEUTRON DIFFRACTIONr_dihedral_angle_other_3_deg3.79610149
NEUTRON DIFFRACTIONr_dihedral_angle_6_deg16.53810117
NEUTRON DIFFRACTIONr_dihedral_angle_other_6_deg13.8991032
NEUTRON DIFFRACTIONr_chiral_restr0.0980.2371
NEUTRON DIFFRACTIONr_gen_planes_refined0.0110.023634
NEUTRON DIFFRACTIONr_gen_planes_other00.02163
NEUTRON DIFFRACTIONr_nbd_refined0.2370.21283
NEUTRON DIFFRACTIONr_symmetry_nbd_other0.1720.21259
NEUTRON DIFFRACTIONr_nbtor_refined0.1880.21288
NEUTRON DIFFRACTIONr_symmetry_nbtor_other0.0420.2109
NEUTRON DIFFRACTIONr_xyhbond_nbd_refined0.1910.2355
NEUTRON DIFFRACTIONr_symmetry_nbd_refined0.3110.272
NEUTRON DIFFRACTIONr_nbd_other0.1920.268
NEUTRON DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.236
NEUTRON DIFFRACTIONr_mcbond_it1.5661.8041588
NEUTRON DIFFRACTIONr_mcbond_other1.5651.8041588
NEUTRON DIFFRACTIONr_mcangle_it2.2243.1362211
NEUTRON DIFFRACTIONr_mcangle_other2.2233.1362212
NEUTRON DIFFRACTIONr_scbond_it2.2852.5232502
NEUTRON DIFFRACTIONr_scbond_other2.3632.1951676
NEUTRON DIFFRACTIONr_scangle_it3.4143.932891
NEUTRON DIFFRACTIONr_scangle_other3.5753.7972482
NEUTRON DIFFRACTIONr_lrange_it5.0927.87110163
NEUTRON DIFFRACTIONr_lrange_other4.79426.369833
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8460.3291180.30225130.30326310.9230.9271000.297
1.846-1.8960.3041440.29323910.29425350.9260.9331000.285
1.896-1.9510.3011210.27823560.27924770.9230.941000.268
1.951-2.010.2851350.26523010.26724360.9370.9461000.254
2.01-2.0760.2941280.24722660.24923940.9380.9551000.228
2.076-2.1480.2451340.22221220.22422560.9620.9631000.201
2.148-2.2280.211920.20721320.20722240.9660.971000.181
2.228-2.3170.2691190.20120000.20521190.9530.9721000.173
2.317-2.4190.2331080.18819410.1920490.9620.9761000.157
2.419-2.5350.241960.17218710.17519670.9580.981000.143
2.535-2.6690.233900.17517890.17818790.9670.981000.142
2.669-2.8280.215760.15917250.16118010.9640.9831000.13
2.828-3.0190.196700.16516100.16616800.9770.9821000.131
3.019-3.2540.242850.16914930.17315790.9660.98199.93670.14
3.254-3.5550.212570.18113950.18314520.9790.9811000.156
3.555-3.9580.215570.17113120.17213700.9760.98699.9270.153
3.958-4.5390.203510.14311260.14511810.9740.98999.66130.122
4.539-5.4840.19410.1339950.13410370.9830.9999.90360.111
5.484-7.4640.246350.168140.1638510.9680.98599.7650.136
7.464-19.4250.332140.1954740.1995620.9450.97886.83270.17

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