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

ID or keywords:

Entry

Database: PDB / ID: 9gyn

Title

Ferredoxin Wild-type - Reduced state

Components

Ferredoxin-1, chloroplastic

Keywords

OXIDOREDUCTASE / 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

Biological species

Spinacia oleracea (spinach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1 Å

Authors

Carr, S.B. / Wei, J. / Vincent, K.A.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/R018413/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/X002624/1	United Kingdom

Citation

Journal: 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

Deposition	Oct 2, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gyn.cif.gz	59.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/9gyn ftp://data.pdbj.org/pub/pdb/validation_reports/gy/9gyn	HTTPS FTP

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Related structure data

Related structure data	9gydC 9gylC 9gyrC 9gyuC 9gz0C 9gz4C 9gzlC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (8) #144 - Dec 2011 Complex I similarity (5) #82 - Oct 2006 Cytochrome p450 similarity (6) #154 - Oct 2012 Citric Acid Cycle similarity (5) #111 - Mar 2009 Hydrogenase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #36 - Dec 2002 Cytochrome c similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (5)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#117 - Sep 2009
Xanthine Oxidoreductase
similarity (8)
#144 - Dec 2011
Complex I
similarity (5)
#82 - Oct 2006
Cytochrome p450
similarity (6)
#154 - Oct 2012
Citric Acid Cycle
similarity (5)
#111 - Mar 2009
Hydrogenase
similarity (4)
#137 - May 2011
Cytochrome bc1
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#36 - Dec 2002
Cytochrome c
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (5)

Deposited unit

AAA: Ferredoxin-1, chloroplastic

hetero molecules

11.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

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 number	19
Space group name H-M	P2₁2₁2₁

#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 interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43 % / Description: Bright red, rhombahedra
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.62 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.62 Å / Relative weight: 1
Reflection	Resolution: 1→39.3 Å / Num. obs: 52421 / % possible obs: 100 % / Redundancy: 24.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.017 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1→1.03 Å / Redundancy: 15.4 % / R_merge(I) obs: 2.5 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2565 / CC_1/2: 0.672 / R_pim(I) all: 0.66 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1→39.321 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.974 / WR_factor R_free: 0.152 / WR_factor R_work: 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

	R_factor	Num. reflection	% reflection
R_free	0.1561	2565	4.904 %
R_work	0.1409	49736	-
all	0.142	-	-
obs	-	52301	99.903 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 16.569 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.525 Å²	0 Å²	0 Å²
2-	-	0.066 Å²	-0 Å²
3-	-	-	-0.591 Å²

Refinement step

Cycle: LAST / Resolution: 1→39.321 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	753	0	4	151	908

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	810
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	711
X-RAY DIFFRACTION	r_angle_refined_deg	2.322	1.647	1114
X-RAY DIFFRACTION	r_angle_other_deg	2.544	1.585	1672
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.025	5	112
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.556	26.829	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.165	15	131
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.254	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	111
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	949
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	158
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	130
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	679
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	400
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	396
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	82
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	23
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.338	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.927	1.482	409
X-RAY DIFFRACTION	r_mcbond_other	3.963	1.475	408
X-RAY DIFFRACTION	r_mcangle_it	4.908	2.207	513
X-RAY DIFFRACTION	r_mcangle_other	4.911	2.22	514
X-RAY DIFFRACTION	r_scbond_it	4.163	1.789	401
X-RAY DIFFRACTION	r_scbond_other	4.192	1.798	398
X-RAY DIFFRACTION	r_scangle_it	4.937	2.583	592
X-RAY DIFFRACTION	r_scangle_other	4.941	2.588	591
X-RAY DIFFRACTION	r_lrange_it	5.148	19.06	901
X-RAY DIFFRACTION	r_lrange_other	5.14	18.292	870
X-RAY DIFFRACTION	r_rigid_bond_restr	15.885	3	1521

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1-1.026	0.304	181	0.276	3643	0.278	3827	0.81	0.812	99.9216	0.264
1.026-1.054	0.211	183	0.222	3529	0.222	3713	0.894	0.885	99.9731	0.203
1.054-1.085	0.195	166	0.19	3450	0.191	3619	0.927	0.924	99.9171	0.167
1.085-1.118	0.183	181	0.168	3344	0.169	3532	0.945	0.931	99.8018	0.145
1.118-1.155	0.164	171	0.148	3225	0.149	3402	0.954	0.961	99.8236	0.127
1.155-1.195	0.149	160	0.131	3132	0.132	3296	0.968	0.972	99.8786	0.113
1.195-1.24	0.135	146	0.126	3057	0.126	3209	0.971	0.971	99.813	0.111
1.24-1.291	0.148	165	0.12	2887	0.121	3060	0.971	0.975	99.7386	0.105
1.291-1.348	0.147	151	0.114	2795	0.116	2950	0.972	0.979	99.8644	0.101
1.348-1.414	0.133	138	0.107	2707	0.109	2848	0.979	0.981	99.8947	0.097
1.414-1.49	0.134	125	0.104	2581	0.105	2710	0.977	0.985	99.8524	0.096
1.49-1.58	0.125	132	0.093	2418	0.094	2551	0.982	0.988	99.9608	0.088
1.58-1.689	0.124	129	0.103	2295	0.104	2424	0.981	0.984	100	0.099
1.689-1.824	0.129	105	0.108	2140	0.109	2246	0.981	0.982	99.9555	0.107
1.824-1.998	0.124	103	0.118	1995	0.118	2098	0.98	0.981	100	0.121
1.998-2.233	0.118	80	0.127	1815	0.126	1895	0.984	0.981	100	0.134
2.233-2.577	0.152	89	0.141	1607	0.141	1696	0.972	0.974	100	0.153
2.577-3.153	0.193	66	0.163	1376	0.164	1442	0.954	0.966	100	0.183
3.153-4.445	0.182	60	0.158	1083	0.159	1143	0.963	0.972	100	0.185
4.445-39.321	0.189	34	0.201	656	0.2	690	0.967	0.961	100	0.235

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