SAXSdb — 1a70

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

FERREDOXIN

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	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

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 1A70	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
9GYR Ferredoxin CNF labelled, oxidised 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 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 sulfate	Resolution 1.10 Å R-free 0.144
9GYR Ferredoxin CNF labelled, oxidised state Deposited 2024-10-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 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 sulfate	Resolution 1.10 Å R-free 0.144
9GYR Ferredoxin CNF labelled, oxidised state Deposited 2024-10-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 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 sulfate	Resolution 1.10 Å R-free 0.144
9GYR Ferredoxin CNF labelled, oxidised state Deposited 2024-10-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 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 sulfate	Resolution 1.10 Å R-free 0.144
9GYU Ferredoxin CNF-labelled reduced state Deposited 2024-10-03	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）	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 13 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 1–97； 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	1a70
Deposition date deposition_date	1998-03-19
Structure title title	SPINACH FERREDOXIN
Keywords keywords	IRON-SULFUR PROTEIN, PHOTOSYNTHESIS, ELECTRON TRANSPORT; IRON-SULFUR PROTEIN
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	13.59 Å
Radius of gyration Rg (electron density) rg_electron	12.16 Å
Forward intensity I(0) i0	2629920.00
Molecular weight molecular_weight	10627.0 kDa
Excluded volume excluded_volume	12957 Å³
Envelope volume envelope_volume	14485 Å³
Hydration-shell volume shell_volume	10197 Å³
Envelope diameter envelope_diameter	38.9 Å
Shell Rg shell_rg	17.85 Å
Envelope Rg envelope_rg	12.39 Å
Shape Rg shape_rg	12.19 Å
Total Rg total_rg	13.32 Å
Total atoms total_atoms	736
Residues n_residues	97
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	42.3 Å
Rg (real space) rg_real	13.48 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	2.6300e+06
I(0) uncertainty (real space) i0_real_error	2.7670e+04
Rg (reciprocal space) rg_reciprocal	13.49 Å
I(0) (reciprocal space) i0_reciprocal	2630000.0000
Solution quality estimate total_estimate	0.8098
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	0.058
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	407200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; 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
Molecular weight formula_weight	10488.5 kDa
Mutation mutation	E92K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	817

AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA

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

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a70a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

CATH v4.4 (1 domains)

Domain ID domain_id	1a70A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

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8. Citations (1)

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Unit-cell length a length_a	31.000 Å
Unit-cell length b length_b	39.180 Å
Unit-cell length c length_c	83.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.1900
R_work r_work	0.1820
R_free r_free	0.2000

fit	/app/data/saxs_computation/a7/1a70/1a70.fit
pddf	/app/data/pr_computation/a7/1a70/1a70.pr.out
profile	/app/data/saxs_computation/a7/1a70/1a70.dat

SPINACH FERREDOXIN

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

FERREDOXIN

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