SAXSdb — 12ss

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

Superoxide dismutase

Cryptosporidium parvum Iowa II

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 26–221 Chain C； UniProt 26–221	Fragment：P26-S221	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D6: 25% (w/v) PEG 3350, 100 mM MES pH 5.5, 200 mM Ammonium acetate. ChtrB.20815.a.B1.PW39484 at 13.5 mg/mL. Metal assigned as Mn acquired from expression. P31 twinned, plate 20585 D6 drop1, Puck: PSL-2101, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.01 Å R-free 0.197
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 26–221 Chain D； UniProt 26–221	Fragment：P26-S221	MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D6: 25% (w/v) PEG 3350, 100 mM MES pH 5.5, 200 mM Ammonium acetate. ChtrB.20815.a.B1.PW39484 at 13.5 mg/mL. Metal assigned as Mn acquired from expression. P31 twinned, plate 20585 D6 drop1, Puck: PSL-2101, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.01 Å R-free 0.197
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 26–221 Chain F； UniProt 26–221	Fragment：P26-S221	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D6: 25% (w/v) PEG 3350, 100 mM MES pH 5.5, 200 mM Ammonium acetate. ChtrB.20815.a.B1.PW39484 at 13.5 mg/mL. Metal assigned as Mn acquired from expression. P31 twinned, plate 20585 D6 drop1, Puck: PSL-2101, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.01 Å R-free 0.197

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A3FQJ9_CRYPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–204； UniProt 26–221 Author chain B； PDBConstruct 9–204； UniProt 26–221 Author chain C； PDBConstruct 9–204； UniProt 26–221 Author chain D； PDBConstruct 9–204； UniProt 26–221 Author chain E； PDBConstruct 9–204； UniProt 26–221 Author chain F； PDBConstruct 9–204； UniProt 26–221

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	12ss
Deposition date deposition_date	2026-04-16
最后修订 last_revision	2026-04-29
Structure title title	Crystal Structure of Superoxide dismutase from Cryptosporidium parvum
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Superoxide dismutase, Cryptosporidium parvum, OXIDOREDUCTASE ;; 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	36.90 Å
Radius of gyration Rg (electron density) rg_electron	36.37 Å
Forward intensity I(0) i0	256444000.00
Molecular weight molecular_weight	132290.0 kDa
Excluded volume excluded_volume	165980 Å³
Envelope volume envelope_volume	212350 Å³
Hydration-shell volume shell_volume	48135 Å³
Envelope diameter envelope_diameter	112.2 Å
Shell Rg shell_rg	43.22 Å
Envelope Rg envelope_rg	35.59 Å
Shape Rg shape_rg	36.33 Å
Total Rg total_rg	36.92 Å
Total atoms total_atoms	9369
Residues n_residues	1173
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	111.6 Å
Rg (real space) rg_real	36.69 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.5640e+08
I(0) uncertainty (real space) i0_real_error	4.0000e+06
Rg (reciprocal space) rg_reciprocal	36.82 Å
I(0) (reciprocal space) i0_reciprocal	256500000.0000
Solution quality estimate total_estimate	0.8401
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.3 Å
Skewness Skewness skewness	0.029
Kurtosis Kurtosis kurtosis	-0.704
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22610000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	Superoxide dismutase
Molecular weight formula_weight	23549.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9621

MAHHHHHHPFELPPLPYDKKALEPVISPETLDYHYGKHHAGYVTKLNSLIKSTEFENETDLMKVIMKSSGPIYNNASQIWNHTFYWSCLRSPSETNKPTSKVSKLIEESFGSFESFKESFTANATGHFGSGWIWVVIDPINNQKLKIVQTHDGDNPEKLGLGKPVLTCDVWEHAYYIDYRNNRGSYVDQFFSIINWDFVESNLS

来源 Source

来源生物 organism	Cryptosporidium parvum Iowa II
NCBI Class编号 ncbi_taxonomy_id	353152
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 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	243

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8. Citations (1)

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Unit-cell length a length_a	92.805 Å
Unit-cell length b length_b	92.805 Å
Unit-cell length c length_c	125.765 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	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	46.400 Å
R factor r_factor	0.1562
R_work r_work	0.1486
R_free r_free	0.1965

fit	/app/data/saxs_computation/2s/12ss/12ss.fit
pddf	/app/data/pr_computation/2s/12ss/12ss.pr.out
profile	/app/data/saxs_computation/2s/12ss/12ss.dat

Crystal Structure of Superoxide dismutase from Cryptosporidium parvum

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

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