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- PDB-9gyr: Ferredoxin CNF labelled, oxidised state -

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Basic information

Entry
Database: PDB / ID: 9gyr
TitleFerredoxin CNF labelled, oxidised 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 Multi-Centre 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 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin-1, chloroplastic
B: Ferredoxin-1, chloroplastic
C: Ferredoxin-1, chloroplastic
D: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8328
Polymers45,1294
Non-polymers7034
Water13,331740
1
A: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,2821
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,2821
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,2821
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,2821
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.834, 61.532, 58.843
Angle α, β, γ (deg.)90.000, 119.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 11282.267 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 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.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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 plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Na K phosphate pH 7-8 2.6-3.6 M Ammonium sulfate
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: 0.77 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 1.1→39.43 Å / Num. obs: 148067 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Net I/σ(I): 11
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7311 / CC1/2: 0.583 / Rpim(I) all: 0.376 / % 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: 1.1→39.42 Å / Cross valid method: FREE R-VALUE / σ(F): 18.79 / Phase error: 14.647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1442 7682 5.19 %
Rwork0.1308 140198 -
obs0.1439 147880 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.57 Å2
Refinement stepCycle: LAST / Resolution: 1.1→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 16 740 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393183
X-RAY DIFFRACTIONf_angle_d0.74844346
X-RAY DIFFRACTIONf_chiral_restr0.0658496
X-RAY DIFFRACTIONf_plane_restr0.0044578
X-RAY DIFFRACTIONf_dihedral_angle_d6.1757455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.120.23964040.22216909X-RAY DIFFRACTION93.73
1.12-1.140.20843380.21217012X-RAY DIFFRACTION95.05
1.14-1.160.21173820.20716924X-RAY DIFFRACTION94.6
1.16-1.190.20233560.19657071X-RAY DIFFRACTION94.96
1.19-1.210.19514460.19636922X-RAY DIFFRACTION93.72
1.21-1.240.19793480.19266988X-RAY DIFFRACTION95.04
1.24-1.270.19993490.18996994X-RAY DIFFRACTION94.9
1.27-1.30.19653730.17737037X-RAY DIFFRACTION94.84
1.3-1.340.17153770.17636922X-RAY DIFFRACTION94.55
1.34-1.390.17234130.16617017X-RAY DIFFRACTION94.39
1.39-1.440.16713840.1647005X-RAY DIFFRACTION94.71
1.44-1.490.15824430.15556960X-RAY DIFFRACTION93.95
1.49-1.560.14264250.14466942X-RAY DIFFRACTION94.22
1.56-1.640.16123860.15037061X-RAY DIFFRACTION94.8
1.64-1.750.14353070.1447102X-RAY DIFFRACTION95.82
1.75-1.880.13813450.14267011X-RAY DIFFRACTION95.28
1.88-2.070.15163730.14857081X-RAY DIFFRACTION95
2.07-2.370.14924020.13447067X-RAY DIFFRACTION94.62
2.37-2.990.15553940.12457042X-RAY DIFFRACTION94.7
2.99-39.420.1514290.11217139X-RAY DIFFRACTION94.12

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