SAXSdb — 1sdy

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

COPPER,ZINC SUPEROXIDE DISMUTASE

Saccharomyces cerevisiae

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–153 Chain B； UniProt 1–153 Chain C； UniProt 1–153 Chain D； UniProt 1–153	Not recorded	CU COPPER (II) ION × 4 ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 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 1SDY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4L 15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE Deposited 1998-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.254
1B4T H48C YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE Deposited 1998-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Mutation：H48C	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.258
1F18 Crystal structure of yeast copper-zinc superoxide dismutase mutant GLY85ARG Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–153（154 aa）	Mutation：G85R	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；275 K；Ammonium Sulfate, Tris-HCl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 275K	Resolution 1.70 Å R-free 0.234
1F1A Crystal structure of yeast H48Q cuznsod fals mutant analog Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–153（154 aa）	Mutation：H48Q	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.233
1F1D Crystal structure of yeast H46C cuznsod mutant Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–153（154 aa）	Mutation：H46C	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；ammonium sulfate, Tris-HCl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.278
1F1G Crystal structure of yeast cuznsod exposed to nitric oxide Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–153（154 aa） Chain B 0–153（154 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.35 Å
1F1G Crystal structure of yeast cuznsod exposed to nitric oxide Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 0–153（154 aa） Chain D 0–153（154 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.35 Å
1F1G Crystal structure of yeast cuznsod exposed to nitric oxide Deposited 2000-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 0–153（154 aa） Chain F 0–153（154 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.35 Å
1JCV REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE LOW TEMPERATURE (-180C) STRUCTURE Deposited 1995-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1JK9 Heterodimer between H48F-ySOD1 and yCCS Deposited 2001-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Mutation：H48F	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；MES, ammonium sulfate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.260
1JK9 Heterodimer between H48F-ySOD1 and yCCS Deposited 2001-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–153（153 aa）	Mutation：H48F	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；MES, ammonium sulfate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.260
1JK9 Heterodimer between H48F-ySOD1 and yCCS Deposited 2001-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–153（153 aa） Chain C 1–153（153 aa）	Mutation：H48F Mutation：H48F	ZN ZINC ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；MES, ammonium sulfate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.260
1JK9 Heterodimer between H48F-ySOD1 and yCCS Deposited 2001-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–153（153 aa） Chain C 1–153（153 aa）	Mutation：H48F Mutation：H48F	ZN ZINC ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；MES, ammonium sulfate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.260
1YAZ AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE Deposited 1998-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 AZI AZIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.208
1YSO YEAST CU, ZN SUPEROXIDE DISMUTASE WITH THE REDUCED BRIDGE BROKEN Deposited 1995-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	CU1 COPPER (I) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.73 Å
2JCW REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE Deposited 1998-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	CU1 COPPER (I) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.70 Å

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SODC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153 Author chain C； PDBConstruct 1–153； UniProt 1–153 Author chain D； PDBConstruct 1–153； UniProt 1–153

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	1sdy
Deposition date deposition_date	1991-06-14
Structure title title	STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE
Keywords keywords	OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR); OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR)
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	29.52 Å
Radius of gyration Rg (electron density) rg_electron	28.54 Å
Forward intensity I(0) i0	73862300.00
Molecular weight molecular_weight	63389.0 kDa
Excluded volume excluded_volume	77564 Å³
Envelope volume envelope_volume	98971 Å³
Hydration-shell volume shell_volume	29748 Å³
Envelope diameter envelope_diameter	105.1 Å
Shell Rg shell_rg	34.82 Å
Envelope Rg envelope_rg	28.34 Å
Shape Rg shape_rg	28.55 Å
Total Rg total_rg	29.10 Å
Total atoms total_atoms	4432
Residues n_residues	600
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	100.3 Å
Rg (real space) rg_real	29.56 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	7.3860e+07
I(0) uncertainty (real space) i0_real_error	1.0290e+06
Rg (reciprocal space) rg_reciprocal	29.54 Å
I(0) (reciprocal space) i0_reciprocal	73860000.0000
Solution quality estimate total_estimate	0.8863
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.306
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10200000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.994

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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	COPPER,ZINC SUPEROXIDE DISMUTASE
Molecular weight formula_weight	15743.4 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4945

VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	513

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1sdya_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1sdyb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1sdyc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1sdyd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1sdyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1sdyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1sdyC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1sdyD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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8. Citations (4)

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Unit-cell length a length_a	105.300 Å
Unit-cell length b length_b	143.000 Å
Unit-cell length c length_c	62.100 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1580
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/sd/1sdy/1sdy.fit
pddf	/app/data/pr_computation/sd/1sdy/1sdy.pr.out
profile	/app/data/saxs_computation/sd/1sdy/1sdy.dat

STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE