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

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Basic information

Entry
Database: PDB / ID: 9kkh
TitleHigh resolution structure of Ferredoxin-NADP+ reductase from maize root - Reduced 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)36,2225
Polymers34,8481
Non-polymers1,3734
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-1 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.080, 59.080, 186.900
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
Components on special symmetry positions
IDModelComponents
11A-1246-

GLY

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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.: 3 / 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.: 510 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
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: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→44.88 Å / Num. obs: 154328 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.33 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.1
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7518 / CC1/2: 0.901

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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: 1.1→44.88 Å / SU ML: 0.0922 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1715 2010 1.3 %
Rwork0.143 152272 -
obs0.1434 154282 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 89 510 3034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523039
X-RAY DIFFRACTIONf_angle_d0.95224160
X-RAY DIFFRACTIONf_chiral_restr0.0849413
X-RAY DIFFRACTIONf_plane_restr0.0079564
X-RAY DIFFRACTIONf_dihedral_angle_d11.2629539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.2261400.196310701X-RAY DIFFRACTION100
1.13-1.160.19131420.161610802X-RAY DIFFRACTION100
1.16-1.190.16271420.142310734X-RAY DIFFRACTION100
1.19-1.230.16481430.13610828X-RAY DIFFRACTION100
1.23-1.270.15631400.145510685X-RAY DIFFRACTION99.97
1.27-1.330.18971410.146110790X-RAY DIFFRACTION99.99
1.33-1.390.18051440.16310811X-RAY DIFFRACTION99.99
1.39-1.460.1681440.129310826X-RAY DIFFRACTION100
1.46-1.550.13551420.127710871X-RAY DIFFRACTION99.99
1.55-1.670.16491440.124910820X-RAY DIFFRACTION99.98
1.67-1.840.16411440.148410955X-RAY DIFFRACTION99.98
1.84-2.10.151430.136910944X-RAY DIFFRACTION100
2.1-2.650.15861480.147911048X-RAY DIFFRACTION99.99
2.65-44.880.19381530.142911457X-RAY DIFFRACTION99.86

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