SAXSdb — 9gyr

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin-1, chloroplastic

Spinacia oleracea

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 51–147	Non-standard monomer：Yes (specific site not provided by mmCIF)	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K phosphate pH 7-8 2.6-3.6 M Ammonium sulfate	Resolution 1.10 Å R-free 0.144
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 51–147	Non-standard monomer：Yes (specific site not provided by mmCIF)	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K phosphate pH 7-8 2.6-3.6 M Ammonium sulfate	Resolution 1.10 Å R-free 0.144
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 51–147	Non-standard monomer：Yes (specific site not provided by mmCIF)	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K phosphate pH 7-8 2.6-3.6 M Ammonium sulfate	Resolution 1.10 Å R-free 0.144
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 51–147	Non-standard monomer：Yes (specific site not provided by mmCIF)	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K phosphate pH 7-8 2.6-3.6 M Ammonium sulfate	Resolution 1.10 Å R-free 0.144

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9GYR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A70 SPINACH FERREDOXIN Deposited 1998-03-19	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Mutation：E92K	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 2.6M AMMONIUM SULPHATE IN 50MM PHOSPHATE BUFFER, PH 7.5	Resolution 1.70 Å R-free 0.200
29KI Spinach Ferredoxin I, Reduced, -400 mV Deposited 2026-03-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.8；277 K；3.5M Ammonium Sulfate, 0.1M Sodium phosphate pH 7.8, 5% Glycerol	Resolution 1.11 Å R-free 0.194
9GYD Ferredoxin Wild-type -As-isolated state Deposited 2024-10-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100 mM Na, K phosphate, 2.6-3.6 M Ammonium phosphate	Resolution 0.92 Å R-free 0.138
9GYL Ferredoxin Wild-type -Oxidised state Deposited 2024-10-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K Phosphate pH 7-8, 26-36 M Ammonium Sulphate	Resolution 1.19 Å R-free 0.178
9GYN Ferredoxin Wild-type - Reduced state Deposited 2024-10-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100 mM Na, K phosphate, 2.6-3.6 M Ammonium phosphate	Resolution 1.00 Å R-free 0.156
9GYU Ferredoxin CNF-labelled reduced state Deposited 2024-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Na K Phosphate pH 7-8 2.6-3.6 M Ammonium Sulphate	Resolution 1.10 Å R-free 0.173
9HI3 C-terminal domain of pectobacterial FusB in complex with spinach ferredoxin 1 Deposited 2024-11-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2 NI NICKEL (II) ION × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05M HEPES,0.05M MOPS pH 7.5, 2M divalent cations (0.005M Manganese(II) chloride, 0.005M Cobalt(II) chloride , 0.005M Nickel(II) chloride, 0.005M Zinc acetate), 0.1 M monosaccharides (0.2 M xylitol, 0.2 M D-fructose, 0.2 M D-sorbitol, 0.2 M myo-inositol, 0.2 M L-rhamnose monohydrate), 20% PEGMME550, 10% PEG 20k	Resolution 1.70 Å R-free 0.205
9TXE Spinach Ferredoxin I, Oxidised Deposited 2026-01-15	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；3.5M Ammonium Sulfate, 0.1M Sodium phosphate pH 7.8, 5% Glycerol	Resolution 0.95 Å R-free 0.178
9TXO Spinach Ferredoxin I, Re-Oxidised Deposited 2026-01-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；277 K；3.5M Ammonium Sulfate, 0.1M Sodium phosphate pH 7.8, 5% Glycerol	Resolution 1.20 Å R-free 0.216
9TXQ Spinach Ferredoxin I, Reduced with Methyl Viologen at -450mV Deposited 2026-01-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–147（97 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；277 K；3.5M Ammonium sulfate, 0.1M Sodium phosphate pH 7.8, 5% Glycerol	Resolution 1.10 Å R-free 0.185

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FER1_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–105； UniProt 51–147 Author chain B； PDBConstruct 9–105； UniProt 51–147 Author chain C； PDBConstruct 9–105； UniProt 51–147 Author chain D； PDBConstruct 9–105； UniProt 51–147

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9gyr
Deposition date deposition_date	2024-10-02
Structure title title	Ferredoxin CNF labelled, oxidised state
Keywords keywords	Metalloprotein Iron-sulfur cluster Electron transfer, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.80 Å
Radius of gyration Rg (electron density) rg_electron	25.15 Å
Forward intensity I(0) i0	37734200.00
Molecular weight molecular_weight	44384.0 kDa
Excluded volume excluded_volume	54029 Å³
Envelope volume envelope_volume	71475 Å³
Hydration-shell volume shell_volume	24130 Å³
Envelope diameter envelope_diameter	102.7 Å
Shell Rg shell_rg	31.56 Å
Envelope Rg envelope_rg	25.02 Å
Shape Rg shape_rg	25.22 Å
Total Rg total_rg	25.66 Å
Total atoms total_atoms	5884
Residues n_residues	400
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	93.0 Å
Rg (real space) rg_real	25.74 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	3.7730e+07
I(0) uncertainty (real space) i0_real_error	6.2550e+05
Rg (reciprocal space) rg_reciprocal	25.76 Å
I(0) (reciprocal space) i0_reciprocal	37730000.0000
Solution quality estimate total_estimate	0.7756
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	36.0 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.335
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9255000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ferredoxin-1, chloroplastic
Molecular weight formula_weight	11282.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6711

GPLGSPEFAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPFSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA

来源 Source

来源生物 organism	Spinacia oleracea
通用名 common_name	spinach
NCBI Class编号 ncbi_taxonomy_id	3562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	740

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8. Citations (1)

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Unit-cell length a length_a	58.834 Å
Unit-cell length b length_b	61.532 Å
Unit-cell length c length_c	58.843 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	39.420 Å
R factor r_factor	0.1439
R_work r_work	0.1308
R_free r_free	0.1442

fit	/app/data/saxs_computation/gy/9gyr/9gyr.fit
pddf	/app/data/pr_computation/gy/9gyr/9gyr.pr.out
profile	/app/data/saxs_computation/gy/9gyr/9gyr.dat

Ferredoxin CNF labelled, oxidised state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin-1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction