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- PDB-9kkg: High resolution structure of Ferredoxin-NADP+ reductase from maiz... -

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Basic information

Entry
Database: PDB / ID: 9kkg
TitleHigh resolution structure 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


chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / photosynthesis / 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: 1.15 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1066
Polymers34,8481
Non-polymers1,2575
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-8 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.290, 59.290, 187.240
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: 34848.461 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→45.02 Å / Num. obs: 136343 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 10.97 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.1
Reflection shellResolution: 1.15→1.17 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6686 / CC1/2: 0.895

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Processing

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

5h59


Resolution: 1.15→45.02 Å / SU ML: 0.0935 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.1738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1585 6811 5 %
Rwork0.142 129525 -
obs0.1428 136336 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.83 Å2
Refinement stepCycle: LAST / Resolution: 1.15→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 83 430 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593001
X-RAY DIFFRACTIONf_angle_d0.94824094
X-RAY DIFFRACTIONf_chiral_restr0.0888414
X-RAY DIFFRACTIONf_plane_restr0.0087552
X-RAY DIFFRACTIONf_dihedral_angle_d9.7203482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.20382270.18114300X-RAY DIFFRACTION99.63
1.16-1.180.18352210.16154175X-RAY DIFFRACTION99.68
1.18-1.190.18772300.1554292X-RAY DIFFRACTION99.65
1.19-1.210.18562230.15214223X-RAY DIFFRACTION99.17
1.21-1.220.14382270.14524263X-RAY DIFFRACTION99.89
1.22-1.240.16432250.14584283X-RAY DIFFRACTION100
1.24-1.260.16412280.1454296X-RAY DIFFRACTION100
1.26-1.280.15542170.14654232X-RAY DIFFRACTION100
1.28-1.30.21042260.16214264X-RAY DIFFRACTION99.98
1.3-1.320.18142200.15374334X-RAY DIFFRACTION100
1.32-1.340.16982260.14314229X-RAY DIFFRACTION100
1.34-1.360.17162260.13784311X-RAY DIFFRACTION100
1.36-1.390.16262300.12874264X-RAY DIFFRACTION99.96
1.39-1.420.1672250.12454292X-RAY DIFFRACTION99.98
1.42-1.450.14462230.124318X-RAY DIFFRACTION99.98
1.45-1.480.15372260.11744305X-RAY DIFFRACTION99.98
1.48-1.520.14922280.12184299X-RAY DIFFRACTION99.93
1.52-1.560.12812250.12264306X-RAY DIFFRACTION99.98
1.56-1.610.14822220.12824312X-RAY DIFFRACTION99.89
1.61-1.660.14062220.12954268X-RAY DIFFRACTION99.84
1.66-1.720.13572290.12734304X-RAY DIFFRACTION99.93
1.72-1.790.14882290.13164338X-RAY DIFFRACTION100
1.79-1.870.14082340.13094335X-RAY DIFFRACTION100
1.87-1.970.14282310.12964321X-RAY DIFFRACTION99.96
1.97-2.090.15752310.13564362X-RAY DIFFRACTION99.98
2.09-2.250.15632240.14044352X-RAY DIFFRACTION99.98
2.25-2.480.13712280.1474404X-RAY DIFFRACTION99.89
2.48-2.840.17872320.15244421X-RAY DIFFRACTION99.83
2.84-3.570.17722320.15094445X-RAY DIFFRACTION99.85
3.57-45.020.15952440.1544677X-RAY DIFFRACTION99.55

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