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- PDB-9gyu: Ferredoxin CNF-labelled reduced state -

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Basic information

Entry
Database: PDB / ID: 9gyu
TitleFerredoxin CNF-labelled reduced state
ComponentsFerredoxin-1, chloroplastic
KeywordsOXIDOREDUCTASE / Metalloprotein Iron-sulfur cluster Electron transfer
Function / homology
Function and homology information


chloroplast stroma / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin-1, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCarr, S.B. / Wei, J. / Vincent, K.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018413/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
CitationJournal: Chembiochem / Year: 2025
Title: Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes.
Authors: Duan, Z. / Wei, J. / Carr, S.B. / Ramirez, M. / Evans, R.M. / Ash, P.A. / Rodriguez-Macia, P. / Sachdeva, A. / Vincent, K.A.
History
DepositionOct 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _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-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,2821
Non-polymers1761
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area5960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.916, 46.761, 63.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ferredoxin-1, chloroplastic / Ferredoxin I / Fd I


Mass: 11282.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ferredoxin with Tyr 37 replaced with cyanophenylalanine (4CF)
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: PETF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00221
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.17 Å3/Da / Density % sol: 43 % / Description: Red rhombahedra
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Na K Phosphate pH 7-8 2.6-3.6 M Ammonium Sulphate
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→53.24 Å / Num. obs: 61312 / % possible obs: 93.9 % / Redundancy: 19 % / Biso Wilson estimate: 9.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.022 / Net I/σ(I): 15.2
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2288 / CC1/2: 0.652 / Rpim(I) all: 0.49 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→31.69 Å / SU ML: 0.0845 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 19.7111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.173 2986 4.87 %
Rwork0.1624 58326 -
obs0.163 61312 90.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.78 Å2
Refinement stepCycle: LAST / Resolution: 1.1→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 4 138 931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077853
X-RAY DIFFRACTIONf_angle_d1.03791171
X-RAY DIFFRACTIONf_chiral_restr0.0836132
X-RAY DIFFRACTIONf_plane_restr0.0085155
X-RAY DIFFRACTIONf_dihedral_angle_d6.2571125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.120.25421180.30532288X-RAY DIFFRACTION74.74
1.12-1.140.29271190.30712352X-RAY DIFFRACTION76.95
1.14-1.160.2871310.27922365X-RAY DIFFRACTION77.81
1.16-1.180.31981130.27842464X-RAY DIFFRACTION80.83
1.18-1.20.26961220.27722490X-RAY DIFFRACTION80.84
1.2-1.230.2721350.26022576X-RAY DIFFRACTION85.66
1.23-1.260.26541480.24222609X-RAY DIFFRACTION84.65
1.26-1.290.23581540.22492672X-RAY DIFFRACTION88.62
1.29-1.330.22091210.21012783X-RAY DIFFRACTION90.52
1.33-1.360.1741450.19032833X-RAY DIFFRACTION92.95
1.36-1.410.20661740.17772911X-RAY DIFFRACTION95.69
1.41-1.460.22711520.172953X-RAY DIFFRACTION96.16
1.46-1.520.15021480.16013012X-RAY DIFFRACTION98.38
1.52-1.590.18651370.14013012X-RAY DIFFRACTION98.53
1.59-1.670.11981430.13292993X-RAY DIFFRACTION97.45
1.67-1.770.15591540.1292981X-RAY DIFFRACTION98
1.77-1.910.14831640.13342972X-RAY DIFFRACTION97.24
1.91-2.10.12311480.12882984X-RAY DIFFRACTION98.09
2.1-2.410.15571430.13023016X-RAY DIFFRACTION97.89
2.41-3.030.1541650.14713000X-RAY DIFFRACTION99.34
3.03-31.690.1511520.14663060X-RAY DIFFRACTION99.66

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