SAXSdb — 3exy

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

Ferredoxin

Allochromatium vinosum

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 2–83	Mutation：V13G	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；277 K；3.5M AMMONIUM SULPHATE, 0.3 M SODIUM CHLORIDE, 0.1 M TRIS , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.48 Å R-free 0.218

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 3EXY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BLU STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM Deposited 1996-04-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–82（82 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 0.1M TRIS-MALEATE BUFFER, PH 6.5 CONTAINING 2.9 M AMMONIUM SULPHATE AND 0.1 M NACL	Resolution 2.10 Å
3EUN Crystal structure of the 2[4Fe-4S] C57A ferredoxin variant from allochromatium vinosum Deposited 2008-10-10	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–83（82 aa）	Mutation：C57A	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；277 K；3.5M AMMONIUM SULPHATE 0.1 M SODIUM CHLORIDE, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.05 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FER_CHRVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–82； UniProt 2–83

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	3exy
Deposition date deposition_date	2008-10-17
Structure title title	Crystal structure of the 2[4Fe-4S] ferredoxin V13G variant from allochromatium vinosum
Keywords keywords	ELECTRON TRANSPORT, FERREDOXIN, [4FE-4S] CLUSTERS, 4Fe-4S, Iron, Iron-sulfur, Metal-binding, Transport; ELECTRON TRANSPORT
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	12.91 Å
Radius of gyration Rg (electron density) rg_electron	12.00 Å
Forward intensity I(0) i0	2642670.00
Molecular weight molecular_weight	9629.0 kDa
Excluded volume excluded_volume	11180 Å³
Envelope volume envelope_volume	12340 Å³
Hydration-shell volume shell_volume	8996 Å³
Envelope diameter envelope_diameter	44.5 Å
Shell Rg shell_rg	17.49 Å
Envelope Rg envelope_rg	12.51 Å
Shape Rg shape_rg	12.20 Å
Total Rg total_rg	12.69 Å
Total atoms total_atoms	633
Residues n_residues	81
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	46.1 Å
Rg (real space) rg_real	12.92 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.6430e+06
I(0) uncertainty (real space) i0_real_error	2.9210e+04
Rg (reciprocal space) rg_reciprocal	12.91 Å
I(0) (reciprocal space) i0_reciprocal	2643000.0000
Solution quality estimate total_estimate	0.8486
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.6 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.219
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	317500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.966

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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	9021.9 kDa
Mutation mutation	V13G
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	812

ALMITDECINCDGCEPECPNGAISQGDETYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPSHEETEDELRAKYERITGEG

来源 Source

来源生物 organism	Allochromatium vinosum
通用名 common_name	Allochromatium vinosum
NCBI Class编号 ncbi_taxonomy_id	1049
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3exya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.1 — Short-chain ferredoxins

CATH v4.4 (1 domains)

Domain ID domain_id	3exyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	51.425 Å
Unit-cell length b length_b	51.425 Å
Unit-cell length c length_c	76.425 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1620
R_work r_work	0.1620
R_free r_free	0.2177

fit	/app/data/saxs_computation/ex/3exy/3exy.fit
pddf	/app/data/pr_computation/ex/3exy/3exy.pr.out
profile	/app/data/saxs_computation/ex/3exy/3exy.dat

Crystal structure of the 2[4Fe-4S] ferredoxin V13G variant from allochromatium vinosum

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