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- PDB-9gyd: Ferredoxin Wild-type -As-isolated state -

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Basic information

Entry
Database: PDB / ID: 9gyd
TitleFerredoxin Wild-type -As-isolated 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: 0.92 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 1, 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)11,4492
Polymers11,2731
Non-polymers1761
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area5530 Å2
Unit cell
Length a, b, c (Å)30.301, 51.410, 61.333
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: 11273.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Wild-type ferredoxin as-isolated state / 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.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: Bright red, rhombahedra
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM Na, K phosphate, 2.6-3.6 M Ammonium phosphate
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.92→39.4 Å / Num. obs: 128152 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Net I/σ(I): 18.2
Reflection shellResolution: 0.92→0.94 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3289 / CC1/2: 0.8 / Rpim(I) all: 0.37 / % possible all: 100

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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: 0.92→39.4 Å / SU ML: 0.094 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.8833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1384 6333 4.94 %
Rwork0.1267 121819 -
obs0.1272 128152 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.86 Å2
Refinement stepCycle: LAST / Resolution: 0.92→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 0 4 147 908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129814
X-RAY DIFFRACTIONf_angle_d1.29091119
X-RAY DIFFRACTIONf_chiral_restr0.1138127
X-RAY DIFFRACTIONf_plane_restr0.0109151
X-RAY DIFFRACTIONf_dihedral_angle_d6.5415122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.930.371870.35574037X-RAY DIFFRACTION99.44
0.93-0.940.33762030.33864101X-RAY DIFFRACTION99.79
0.94-0.950.29682050.29464059X-RAY DIFFRACTION99.95
0.95-0.960.28541980.26644079X-RAY DIFFRACTION99.95
0.96-0.980.27122000.2474063X-RAY DIFFRACTION99.56
0.98-0.990.21762350.22014017X-RAY DIFFRACTION99.81
0.99-1.010.23422110.20564114X-RAY DIFFRACTION99.91
1.01-1.020.232200.19823999X-RAY DIFFRACTION99.98
1.02-1.040.2022190.16624074X-RAY DIFFRACTION100
1.04-1.050.15212220.15894107X-RAY DIFFRACTION100
1.05-1.070.16131900.13644071X-RAY DIFFRACTION99.98
1.07-1.090.1482280.12644089X-RAY DIFFRACTION99.91
1.09-1.110.12162280.1164009X-RAY DIFFRACTION99.76
1.11-1.130.13042420.11554020X-RAY DIFFRACTION99.93
1.13-1.160.10782110.10894098X-RAY DIFFRACTION99.84
1.16-1.190.11782140.1044037X-RAY DIFFRACTION99.79
1.19-1.220.11861990.10454092X-RAY DIFFRACTION99.95
1.22-1.250.11811990.10274068X-RAY DIFFRACTION99.93
1.25-1.290.12342130.10034043X-RAY DIFFRACTION99.77
1.29-1.330.12082240.0984066X-RAY DIFFRACTION99.79
1.33-1.370.10542220.09864075X-RAY DIFFRACTION99.88
1.37-1.430.11662100.09774076X-RAY DIFFRACTION99.84
1.43-1.490.10512060.09584071X-RAY DIFFRACTION99.95
1.49-1.570.09892260.09074043X-RAY DIFFRACTION99.95
1.57-1.670.11131770.08954094X-RAY DIFFRACTION99.98
1.67-1.80.12062210.10284074X-RAY DIFFRACTION100
1.8-1.980.12351890.11054095X-RAY DIFFRACTION100
1.98-2.270.12712230.11824056X-RAY DIFFRACTION100
2.27-2.860.14932360.13914053X-RAY DIFFRACTION100
2.86-39.40.15571750.1473939X-RAY DIFFRACTION96.21

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