SAXSdb — 1dfx

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

DESULFOFERRODOXIN

OrganismNot specified

UniProt P22076

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–125	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 0.1 M HEPES, CACL2 0.2 M, PH 7.5	Resolution 1.90 Å R-free 0.230

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DESR_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125

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	1dfx
Deposition date deposition_date	1997-09-03
Structure title title	DESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774
Keywords keywords	ELECTRON TRANSPORT, NON-HEME IRON PROTEIN; 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	15.72 Å
Radius of gyration Rg (electron density) rg_electron	14.52 Å
Forward intensity I(0) i0	4058490.00
Molecular weight molecular_weight	14028.0 kDa
Excluded volume excluded_volume	17413 Å³
Envelope volume envelope_volume	19850 Å³
Hydration-shell volume shell_volume	11871 Å³
Envelope diameter envelope_diameter	53.1 Å
Shell Rg shell_rg	19.85 Å
Envelope Rg envelope_rg	14.91 Å
Shape Rg shape_rg	14.47 Å
Total Rg total_rg	15.73 Å
Total atoms total_atoms	977
Residues n_residues	125
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	53.9 Å
Rg (real space) rg_real	15.67 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.0580e+06
I(0) uncertainty (real space) i0_real_error	4.3030e+04
Rg (reciprocal space) rg_reciprocal	15.67 Å
I(0) (reciprocal space) i0_reciprocal	4059000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	761900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DESULFOFERRODOXIN
Molecular weight formula_weight	13903.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1048

PKHLEVYKCTHCGNIVEVLHGGGAELVCCGEPMKHMVEGSTDGAMEKHVPVIEKVDGGYLIKVGSVPHPMEEKHWIEWIELLADGRSYTKFLKPGDAPEAFFAIDASKVTAREYCNLHGHWKAEN

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dfxa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.13 — Superoxide reductase-like
Family Family family	b.1.13.1 — Superoxide reductase-like

Domain ID domain_id	d1dfxa2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.2 — Desulforedoxin

CATH v4.4 (1 domains)

Domain ID domain_id	1dfxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	730 — SOR catalytic domain

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8. Citations (2)

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Unit-cell length a length_a	112.500 Å
Unit-cell length b length_b	112.500 Å
Unit-cell length c length_c	63.200 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2000
R_work r_work	—
R_free r_free	0.2300

fit	/app/data/saxs_computation/df/1dfx/1dfx.fit
pddf	/app/data/pr_computation/df/1dfx/1dfx.pr.out
profile	/app/data/saxs_computation/df/1dfx/1dfx.dat

DESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774

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

DESULFOFERRODOXIN

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