SAXSdb — 1yai

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

COPPER, ZINC SUPEROXIDE DISMUTASE

Photobacterium leiognathi

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 23–173	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；42% MPD, 60 MM POTASSIUM PHOSPHATE, PH 6.5	Resolution 1.90 Å R-free 0.210
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 23–173 Chain C； UniProt 23–173	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；42% MPD, 60 MM POTASSIUM PHOSPHATE, PH 6.5	Resolution 1.90 Å R-free 0.210

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 1YAI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BZO THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY. Deposited 1998-11-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2 IUM URANYL (VI) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, T=28C	Resolution 2.10 Å
1IB5 X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83Y Deposited 2001-03-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：W83Y	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；301 K；PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.45 Å R-free 0.265
1IBB X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83F Deposited 2001-03-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：W83F	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；301 K；PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.10 Å R-free 0.210
1IBD X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A Deposited 2001-03-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：V29A	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；301 K；PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.00 Å R-free 0.269
1IBF X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G Deposited 2001-03-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：V29G	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；301 K；PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.20 Å R-free 0.278
1IBH X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT M41I Deposited 2001-03-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：M41I	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；301 K；PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.00 Å R-free 0.287
1OAJ Active site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase Deposited 2003-01-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：YES	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；301 K；PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, TEMPERATURE 28C	Resolution 1.73 Å R-free 0.231
1OAL Active site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase Deposited 2003-01-15	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–173（151 aa）	Mutation：YES	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；301 K；PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, T=28C	Resolution 1.50 Å R-free 0.194

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SODC_PHOLE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 23–173 Author chain B； PDBConstruct 1–151； UniProt 23–173 Author chain C； PDBConstruct 1–151； UniProt 23–173

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	1yai
Deposition date deposition_date	1996-02-03
Structure title title	X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE
Keywords keywords	OXIDOREDUCTASE, BETA-BARREL, METALLOENZYME, MACROMOLECULAR ASSEMBLY; OXIDOREDUCTASE
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	27.02 Å
Radius of gyration Rg (electron density) rg_electron	26.58 Å
Forward intensity I(0) i0	41012600.00
Molecular weight molecular_weight	47531.0 kDa
Excluded volume excluded_volume	58496 Å³
Envelope volume envelope_volume	75806 Å³
Hydration-shell volume shell_volume	24047 Å³
Envelope diameter envelope_diameter	87.1 Å
Shell Rg shell_rg	33.60 Å
Envelope Rg envelope_rg	26.02 Å
Shape Rg shape_rg	26.60 Å
Total Rg total_rg	27.26 Å
Total atoms total_atoms	3320
Residues n_residues	452
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	81.1 Å
Rg (real space) rg_real	26.98 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.1010e+07
I(0) uncertainty (real space) i0_real_error	6.0870e+05
Rg (reciprocal space) rg_reciprocal	27.00 Å
I(0) (reciprocal space) i0_reciprocal	41010000.0000
Solution quality estimate total_estimate	0.9093
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.143
Kurtosis Kurtosis kurtosis	-0.789
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4917000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.952

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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	15801.8 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3678

QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ

来源 Source

来源生物 organism	Photobacterium leiognathi
NCBI Class编号 ncbi_taxonomy_id	658
宿主生物 host_organism	Escherichia coli

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	3

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	358

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1yaia_
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	d1yaib_
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	d1yaic_
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 (3 domains)

Domain ID domain_id	1yaiA00
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	1yaiB00
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	1yaiC00
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 (2)

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Unit-cell length a length_a	120.700 Å
Unit-cell length b length_b	87.000 Å
Unit-cell length c length_c	43.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1490
R_free r_free	0.2100

fit	/app/data/saxs_computation/ya/1yai/1yai.fit
pddf	/app/data/pr_computation/ya/1yai/1yai.pr.out
profile	/app/data/saxs_computation/ya/1yai/1yai.dat

X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE

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

COPPER, ZINC SUPEROXIDE DISMUTASE

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