SAXSdb — 1qyb

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

Rubrerythrin

Desulfovibrio vulgaris subsp. vulgaris

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 1–191	Not recorded	FE FE (III) ION × 4 ZN ZINC ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG1450, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.213
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–191	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG1450, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.213

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 1QYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B71 RUBRERYTHRIN Deposited 1999-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 1.90 Å
1B71 RUBRERYTHRIN Deposited 1999-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 1.90 Å
1DVB RUBRERYTHRIN Deposited 2000-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；PEG4000, Tris acid maleate, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 1.90 Å R-free 0.255
1DVB RUBRERYTHRIN Deposited 2000-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；PEG4000, Tris acid maleate, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 1.90 Å R-free 0.255
1JYB Crystal structure of Rubrerythrin Deposited 2001-09-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG1500, Tris, pH 7.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.231
1JYB Crystal structure of Rubrerythrin Deposited 2001-09-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG1500, Tris, pH 7.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.231
1LKM Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 1450, Tris, Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.69 Å R-free 0.210
1LKM Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 1450, Tris, Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.69 Å R-free 0.210
1LKO Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	FE2 FE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG1450, Tris, Sodium Dithionite, NADH, BenC, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.204
1LKO Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE2 FE (II) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG1450, Tris, Sodium Dithionite, NADH, BenC, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.204
1LKP Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	AZI AZIDE ION × 4 FE2 FE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, MOPS, Sodium Azide, Sodium Dithionite, NADH, BenC, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.64 Å R-free 0.202
1LKP Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	AZI AZIDE ION × 8 FE2 FE (II) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, MOPS, Sodium Azide, Sodium Dithionite, NADH, BenC, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.64 Å R-free 0.202
1RYT RUBRERYTHRIN Deposited 1996-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa）	Not recorded	FE FE (III) ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.256
1RYT RUBRERYTHRIN Deposited 1996-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–191（190 aa）	Not recorded	FE FE (III) ION × 12	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.256
1S2Z X-ray crystal structure of Desulfovibrio vulgaris Rubrerythrin with displacement of iron by zinc at the diiron Site Deposited 2004-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.196
1S2Z X-ray crystal structure of Desulfovibrio vulgaris Rubrerythrin with displacement of iron by zinc at the diiron Site Deposited 2004-01-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.196
1S30 X-ray crystal structure of Desulfovibrio vulgaris Rubrerythrin with displacement of iron by zinc at the diiron Site Deposited 2004-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.05 Å R-free 0.208
1S30 X-ray crystal structure of Desulfovibrio vulgaris Rubrerythrin with displacement of iron by zinc at the diiron Site Deposited 2004-01-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–191（191 aa）	Not recorded	FE FE (III) ION × 8 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 1450, Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.05 Å R-free 0.208

9 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RUBY_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191

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	1qyb
Deposition date deposition_date	2003-09-10
Structure title title	X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures
Keywords keywords	Rubrerythrin, zinc-substituted, diiron four-helix bundle, rubredoxin-like, 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	20.05 Å
Radius of gyration Rg (electron density) rg_electron	19.69 Å
Forward intensity I(0) i0	9168140.00
Molecular weight molecular_weight	21683.0 kDa
Excluded volume excluded_volume	26739 Å³
Envelope volume envelope_volume	32235 Å³
Hydration-shell volume shell_volume	14905 Å³
Envelope diameter envelope_diameter	66.3 Å
Shell Rg shell_rg	24.17 Å
Envelope Rg envelope_rg	19.93 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.50 Å
Total atoms total_atoms	1522
Residues n_residues	190
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	66.9 Å
Rg (real space) rg_real	20.21 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	9.1680e+06
I(0) uncertainty (real space) i0_real_error	1.2130e+05
Rg (reciprocal space) rg_reciprocal	20.18 Å
I(0) (reciprocal space) i0_reciprocal	9168000.0000
Solution quality estimate total_estimate	0.8610
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.539
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1224000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.921

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Rubrerythrin
Molecular weight formula_weight	21577.3 kDa
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	1770

MKSLKGSRTEKNILTAFAGESQARNRYNYFGGQAKKDGFVQISDIFAETADQEREHAKRLFKFLEGGDLEIVAAFPAGIIADTHANLIASAAGEHHEYTEMYPSFARIAREEGYEEIARVFASIAVAEEFHEKRFLDFARNIKEGRVFLREQATKWRCRNCGYVHEGTGAPELCPACAHPKAHFELLGINW

来源 Source

来源生物 organism	Desulfovibrio vulgaris subsp. vulgaris
NCBI Class编号 ncbi_taxonomy_id	882
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1qyba1
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d1qyba2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.1 — Rubredoxin

CATH v4.4 (2 domains)

Domain ID domain_id	1qybA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	1qybA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	48.008 Å
Unit-cell length b length_b	80.161 Å
Unit-cell length c length_c	101.029 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	17.590 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2130

fit	/app/data/saxs_computation/qy/1qyb/1qyb.fit
pddf	/app/data/pr_computation/qy/1qyb/1qyb.pr.out
profile	/app/data/saxs_computation/qy/1qyb/1qyb.dat

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures

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

Rubrerythrin

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