SAXSdb — 1dxg

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

DESULFOREDOXIN

OrganismNot specified

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 1–36 Chain B； UniProt 1–36	Not recorded	FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；10% PEG 4K, 0.1M SODIUM ACETATE (PH 4.5)	Resolution 1.80 Å R-free 0.187

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 1DXG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFW GA-SUBSTITUTED DESULFOREDOXIN Deposited 1999-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–37（36 aa） Chain B 2–37（36 aa）	Not recorded	GA GALLIUM (III) ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 1.90 Å
1DCD DESULFOREDOXIN COMPLEXED WITH CD2+ Deposited 1999-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–37（36 aa） Chain B 2–37（36 aa）	Not recorded	CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；30% ETHANOL, 0.1 M SODIUM ACETATE PH 5, 0.2 M CACL2, pH 5.0	Resolution 2.00 Å
1DHG HG-SUBSTITUTED DESULFOREDOXIN Deposited 1999-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–37（36 aa） Chain B 2–37（36 aa）	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.50 Å
2LK5 Solution structure of the Zn(II) form of Desulforedoxin Deposited 2011-10-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–37（36 aa） Chain B 2–37（36 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2-4 mM protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LK6 NMR determination of the global structure of the Cd-113 derivative of desulforedoxin Deposited 2011-10-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–37（36 aa） Chain B 2–37（36 aa）	Not recorded	CD CADMIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 10 mM potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DESR_DESGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–36； UniProt 1–36 Author chain B； PDBConstruct 1–36； UniProt 1–36

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	1dxg
Deposition date deposition_date	1997-07-04
Structure title title	CRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS AT 1.8 A RESOLUTION
Keywords keywords	NON-HEME IRON PROTEIN, RUBREDOXIN TYPE METAL CENTER, ELECTRON TRANSPORT; NON-HEME IRON 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	11.92 Å
Radius of gyration Rg (electron density) rg_electron	10.56 Å
Forward intensity I(0) i0	1538780.00
Molecular weight molecular_weight	7712.0 kDa
Excluded volume excluded_volume	9338 Å³
Envelope volume envelope_volume	10151 Å³
Hydration-shell volume shell_volume	8271 Å³
Envelope diameter envelope_diameter	32.3 Å
Shell Rg shell_rg	16.05 Å
Envelope Rg envelope_rg	10.87 Å
Shape Rg shape_rg	10.58 Å
Total Rg total_rg	11.87 Å
Total atoms total_atoms	524
Residues n_residues	72
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	35.5 Å
Rg (real space) rg_real	11.83 Å
Rg uncertainty (real space) rg_real_error	0.19 Å
I(0) (real space) i0_real	1.5390e+06
I(0) uncertainty (real space) i0_real_error	1.5230e+04
Rg (reciprocal space) rg_reciprocal	11.84 Å
I(0) (reciprocal space) i0_reciprocal	1539000.0000
Solution quality estimate total_estimate	0.9041
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.047
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	177200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dxga_
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

Domain ID domain_id	d1dxgb_
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

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8. Citations (1)

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Unit-cell length a length_a	42.180 Å
Unit-cell length b length_b	42.180 Å
Unit-cell length c length_c	72.220 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1690
R_work r_work	0.1690
R_free r_free	0.1870

Description description	DESULFOREDOXIN
Molecular weight formula_weight	3807.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	593

CRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS AT 1.8 A RESOLUTION

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

DESULFOREDOXIN

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

fit	/app/data/saxs_computation/dx/1dxg/1dxg.fit
pddf	/app/data/pr_computation/dx/1dxg/1dxg.pr.out
profile	/app/data/saxs_computation/dx/1dxg/1dxg.dat