SAXSdb — 1dcd

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

PROTEIN (DESULFOREDOXIN)

Desulfovibrio gigas

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 2–37 Chain B； UniProt 2–37	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

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 1DCD	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 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
1DHG HG-SUBSTITUTED DESULFOREDOXIN Deposited 1999-03-22	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
1DXG CRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS AT 1.8 A RESOLUTION Deposited 1997-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–36（36 aa） Chain B 1–36（36 aa）	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
2LK5 Solution structure of the Zn(II) form of Desulforedoxin Deposited 2011-10-06	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 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 2–37 Author chain B； PDBConstruct 1–36； UniProt 2–37

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	1dcd
Deposition date deposition_date	1999-03-20
Structure title title	DESULFOREDOXIN COMPLEXED WITH CD2+
Keywords keywords	RUBREDOXIN TYPE PROTEIN, ELECTRON 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	11.90 Å
Radius of gyration Rg (electron density) rg_electron	10.56 Å
Forward intensity I(0) i0	1645310.00
Molecular weight molecular_weight	7825.0 kDa
Excluded volume excluded_volume	9354 Å³
Envelope volume envelope_volume	10254 Å³
Hydration-shell volume shell_volume	8318 Å³
Envelope diameter envelope_diameter	32.2 Å
Shell Rg shell_rg	16.06 Å
Envelope Rg envelope_rg	10.92 Å
Shape Rg shape_rg	10.59 Å
Total Rg total_rg	11.83 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	35.4 Å
Rg (real space) rg_real	11.81 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	1.6450e+06
I(0) uncertainty (real space) i0_real_error	1.5960e+04
Rg (reciprocal space) rg_reciprocal	11.81 Å
I(0) (reciprocal space) i0_reciprocal	1645000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.032
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	131500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.954

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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	PROTEIN (DESULFOREDOXIN)
Molecular weight formula_weight	3807.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	581

ANEGDVYKCELCGQVVKVLEEGGGTLVCCGEDMVKQ

来源 Source

来源生物 organism	Desulfovibrio gigas
NCBI Class编号 ncbi_taxonomy_id	879
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 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	53

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dcda_
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	d1dcdb_
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 (2)

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Unit-cell length a length_a	27.950 Å
Unit-cell length b length_b	27.950 Å
Unit-cell length c length_c	130.940 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	14.800 Å
R factor r_factor	0.1890
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/dc/1dcd/1dcd.fit
pddf	/app/data/pr_computation/dc/1dcd/1dcd.pr.out
profile	/app/data/saxs_computation/dc/1dcd/1dcd.dat

DESULFOREDOXIN COMPLEXED WITH CD2+

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

PROTEIN (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