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- PDB-9gyn: Ferredoxin Wild-type - Reduced state -

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Basic information

Entry
Database: PDB / ID: 9gyn
TitleFerredoxin Wild-type - 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 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)11,4492
Polymers11,2731
Non-polymers1761
Water2,720151
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 area5460 Å2
Unit cell
Length a, b, c (Å)30.286, 51.285, 61.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
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: isolated from a natural source / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 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→39.3 Å / Num. obs: 52421 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.017 / Net I/σ(I): 15.7
Reflection shellResolution: 1→1.03 Å / Redundancy: 15.4 % / Rmerge(I) obs: 2.5 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2565 / CC1/2: 0.672 / Rpim(I) all: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→39.321 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.137 / Average fsc free: 0.9507 / Average fsc work: 0.9512 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1561 2565 4.904 %
Rwork0.1409 49736 -
all0.142 --
obs-52301 99.903 %
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: 16.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.525 Å20 Å20 Å2
2--0.066 Å2-0 Å2
3----0.591 Å2
Refinement stepCycle: LAST / Resolution: 1→39.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 4 151 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013810
X-RAY DIFFRACTIONr_bond_other_d0.0360.017711
X-RAY DIFFRACTIONr_angle_refined_deg2.3221.6471114
X-RAY DIFFRACTIONr_angle_other_deg2.5441.5851672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55626.82941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16515131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.254151
X-RAY DIFFRACTIONr_chiral_restr0.1410.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02949
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02158
X-RAY DIFFRACTIONr_nbd_refined0.2390.2130
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.2679
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2400
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.282
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.23
X-RAY DIFFRACTIONr_nbd_other0.170.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3380.215
X-RAY DIFFRACTIONr_mcbond_it3.9271.482409
X-RAY DIFFRACTIONr_mcbond_other3.9631.475408
X-RAY DIFFRACTIONr_mcangle_it4.9082.207513
X-RAY DIFFRACTIONr_mcangle_other4.9112.22514
X-RAY DIFFRACTIONr_scbond_it4.1631.789401
X-RAY DIFFRACTIONr_scbond_other4.1921.798398
X-RAY DIFFRACTIONr_scangle_it4.9372.583592
X-RAY DIFFRACTIONr_scangle_other4.9412.588591
X-RAY DIFFRACTIONr_lrange_it5.14819.06901
X-RAY DIFFRACTIONr_lrange_other5.1418.292870
X-RAY DIFFRACTIONr_rigid_bond_restr15.88531521
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
1-1.0260.3041810.27636430.27838270.810.81299.92160.264
1.026-1.0540.2111830.22235290.22237130.8940.88599.97310.203
1.054-1.0850.1951660.1934500.19136190.9270.92499.91710.167
1.085-1.1180.1831810.16833440.16935320.9450.93199.80180.145
1.118-1.1550.1641710.14832250.14934020.9540.96199.82360.127
1.155-1.1950.1491600.13131320.13232960.9680.97299.87860.113
1.195-1.240.1351460.12630570.12632090.9710.97199.8130.111
1.24-1.2910.1481650.1228870.12130600.9710.97599.73860.105
1.291-1.3480.1471510.11427950.11629500.9720.97999.86440.101
1.348-1.4140.1331380.10727070.10928480.9790.98199.89470.097
1.414-1.490.1341250.10425810.10527100.9770.98599.85240.096
1.49-1.580.1251320.09324180.09425510.9820.98899.96080.088
1.58-1.6890.1241290.10322950.10424240.9810.9841000.099
1.689-1.8240.1291050.10821400.10922460.9810.98299.95550.107
1.824-1.9980.1241030.11819950.11820980.980.9811000.121
1.998-2.2330.118800.12718150.12618950.9840.9811000.134
2.233-2.5770.152890.14116070.14116960.9720.9741000.153
2.577-3.1530.193660.16313760.16414420.9540.9661000.183
3.153-4.4450.182600.15810830.15911430.9630.9721000.185
4.445-39.3210.189340.2016560.26900.9670.9611000.235

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