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- PDB-9gyl: Ferredoxin Wild-type -Oxidised state -

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Basic information

Entry
Database: PDB / ID: 9gyl
TitleFerredoxin Wild-type -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: 1.19 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 2, 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
Revision 1.2Jul 30, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5453
Polymers11,2731
Non-polymers2722
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-23 kcal/mol
Surface area5510 Å2
Unit cell
Length a, b, c (Å)62.050, 62.050, 85.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-202-

SO4

21AAA-422-

HOH

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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 protein sequence, iron sulfur cluster oxidised with potassium ferricyanide
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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, sitting drop
Details: 100 mM Na K Phosphate pH 7-8, 26-36 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: I04 / Wavelength: 0.62 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.19→50.232 Å / Num. obs: 54217 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.02 / Net I/σ(I): 14.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 24.3 % / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2631 / CC1/2: 0.378 / Rpim(I) all: 0.93 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→50.232 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.332 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.178 2709 5.005 %
Rwork0.1557 51413 -
all0.157 --
obs-54122 99.956 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.19→50.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 16 134 903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.013802
X-RAY DIFFRACTIONr_bond_other_d0.0010.017697
X-RAY DIFFRACTIONr_angle_refined_deg2.3581.651097
X-RAY DIFFRACTIONr_angle_other_deg1.641.5891632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72326.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62115125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.304151
X-RAY DIFFRACTIONr_chiral_restr0.1230.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02153
X-RAY DIFFRACTIONr_nbd_refined0.2830.2139
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.2665
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2397
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.23
X-RAY DIFFRACTIONr_nbd_other0.1260.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.28
X-RAY DIFFRACTIONr_mcbond_it2.3891.618407
X-RAY DIFFRACTIONr_mcbond_other1.7431.612406
X-RAY DIFFRACTIONr_mcangle_it1.9182.426508
X-RAY DIFFRACTIONr_mcangle_other2.2422.433509
X-RAY DIFFRACTIONr_scbond_it3.5962.025395
X-RAY DIFFRACTIONr_scbond_other3.6182.036388
X-RAY DIFFRACTIONr_scangle_it3.5972.912585
X-RAY DIFFRACTIONr_scangle_other3.5892.918578
X-RAY DIFFRACTIONr_lrange_it3.72421.801891
X-RAY DIFFRACTIONr_lrange_other3.52820.974859
X-RAY DIFFRACTIONr_rigid_bond_restr4.96331499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.19-1.2210.362310.37236600.37139110.520.5499.48860.369
1.221-1.2550.3841930.36736470.36738410.5710.58899.9740.366
1.255-1.2910.3092030.32835590.32737630.6210.63599.97340.327
1.291-1.3310.3221620.28434450.28536070.750.7661000.281
1.331-1.3740.2491710.24933690.24935400.8520.861000.242
1.374-1.4220.251810.19932250.20234060.880.9061000.185
1.422-1.4760.2091610.17131630.17233250.9230.93799.96990.149
1.476-1.5360.1671610.13629980.13731590.9540.9591000.112
1.536-1.6050.1391440.11429030.11530480.970.97399.96720.092
1.605-1.6830.121320.09628180.09729500.9790.9821000.077
1.683-1.7740.1241530.0926440.09227970.9810.9861000.073
1.774-1.8810.1351490.09725030.09926520.9780.9831000.081
1.881-2.0110.1571260.11323760.11525020.9750.9811000.099
2.011-2.1720.144960.12222250.12323210.9770.9811000.109
2.172-2.3780.1531110.11920570.12121680.9770.9821000.106
2.378-2.6580.124960.1218750.1219710.9820.981000.108
2.658-3.0680.178680.16416830.16517510.9610.9681000.153
3.068-3.7540.229730.16714330.1715060.9560.9691000.163
3.754-5.2950.141620.15211400.15112020.9850.9821000.158
5.295-50.2320.232360.2426900.2427260.9640.9521000.249

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