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

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Basic information

Entry
Database: PDB / ID: 9kkc
TitleNeutron structure of Ferredoxin-NADP+ reductase from maize root -Oxidized 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
FLAVIN-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)35,5853
Polymers34,6041
Non-polymers9812
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.29, 59.29, 187.24
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-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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: Mar 2, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.051
25.381
ReflectionResolution: 1.8→19.415 Å / Num. obs: 36250 / % possible obs: 99.5 % / Redundancy: 9.0226 % / CC1/2: 0.9682 / Rpim(I) all: 0.1548 / Net I/σ(I): 6.34
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3539 / CC1/2: 0.3492 / Rpim(I) all: 0.718

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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→19.415 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.225 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.164
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2449 1764 4.866 %
Rwork0.1904 34484 -
all0.193 --
obs-36248 99.577 %
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: 24.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å20.022 Å2-0 Å2
2--0.043 Å2-0 Å2
3----0.141 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
NEUTRON DIFFRACTIONr_bond_refined_d0.0080.0144205
NEUTRON DIFFRACTIONr_bond_other_d0.0010.0171975
NEUTRON DIFFRACTIONr_ext_dist_refined_b00.0057752
NEUTRON DIFFRACTIONr_angle_refined_deg1.6782.0145201
NEUTRON DIFFRACTIONr_angle_other_deg0.5641.7084810
NEUTRON DIFFRACTIONr_dihedral_angle_1_deg6.4435327
NEUTRON DIFFRACTIONr_dihedral_angle_2_deg8.06110643.24594
NEUTRON DIFFRACTIONr_dihedral_angle_3_deg14.95810522
NEUTRON DIFFRACTIONr_dihedral_angle_other_3_deg3.89510153
NEUTRON DIFFRACTIONr_dihedral_angle_6_deg16.48110122
NEUTRON DIFFRACTIONr_dihedral_angle_other_6_deg14.5111031
NEUTRON DIFFRACTIONr_chiral_restr0.0880.2375
NEUTRON DIFFRACTIONr_gen_planes_refined0.0110.023686
NEUTRON DIFFRACTIONr_gen_planes_other00.02163
NEUTRON DIFFRACTIONr_nbd_refined0.2180.21267
NEUTRON DIFFRACTIONr_symmetry_nbd_other0.1630.21232
NEUTRON DIFFRACTIONr_nbtor_refined0.1830.21217
NEUTRON DIFFRACTIONr_symmetry_nbtor_other0.0530.299
NEUTRON DIFFRACTIONr_xyhbond_nbd_refined0.1980.2379
NEUTRON DIFFRACTIONr_symmetry_nbd_refined0.2280.271
NEUTRON DIFFRACTIONr_nbd_other0.1940.266
NEUTRON DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.243
NEUTRON DIFFRACTIONr_mcbond_it1.7271.9541610
NEUTRON DIFFRACTIONr_mcbond_other1.7271.9541610
NEUTRON DIFFRACTIONr_mcangle_it2.3923.3962240
NEUTRON DIFFRACTIONr_mcangle_other2.3923.3962241
NEUTRON DIFFRACTIONr_scbond_it2.4282.7312595
NEUTRON DIFFRACTIONr_scbond_other2.5292.3691699
NEUTRON DIFFRACTIONr_scangle_it3.6964.2472961
NEUTRON DIFFRACTIONr_scangle_other3.8954.1072515
NEUTRON DIFFRACTIONr_lrange_it5.37731.34510076
NEUTRON DIFFRACTIONr_lrange_other5.05229.6179686
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
1.8-1.8460.3091130.31724830.31626100.930.92299.46360.31
1.846-1.8960.2951460.29224130.29225640.930.93199.8050.282
1.896-1.9510.2841210.27523170.27524420.9390.94399.83620.262
1.951-2.010.2941340.25822840.2624190.9340.94999.95870.242
2.01-2.0750.2761310.23122420.23423750.9440.9699.91580.21
2.075-2.1470.2281320.21621520.21722850.9650.96699.95620.191
2.147-2.2270.243940.20521050.20721990.9520.971000.176
2.227-2.3170.2361150.1919890.19321040.9560.9741000.161
2.317-2.4190.2531080.19119580.19520660.9550.9761000.157
2.419-2.5350.241940.17318560.17619500.9630.981000.14
2.535-2.6690.248920.17418000.17818920.9670.9811000.141
2.669-2.8280.205750.16916950.17117710.970.98299.94350.136
2.828-3.0190.236690.1616160.16316850.9660.9831000.124
3.019-3.2540.209850.15314740.15615590.9710.9851000.127
3.254-3.5540.24570.17214020.17514600.9690.98499.93150.149
3.554-3.9570.193570.15612920.15713540.9770.98799.63070.135
3.957-4.5380.217510.13811260.14111800.9770.9999.74580.115
4.538-5.4840.233410.12810020.13110430.9750.9911000.106
5.484-7.4630.242350.1458040.1498410.9750.98899.76220.117
7.463-19.4150.288140.1754740.1785620.9430.98186.83270.147

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