SAXSdb — 1avm

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

SUPEROXIDE DISMUTASE

Propionibacterium freudenreichii subsp. shermanii

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 1–201 Chain B； UniProt 1–201	Not recorded	FE FE (III) ION × 4 AZI AZIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：vapor diffusion - hanging drop - microseeding；pH 6.15；277 K；FROM 2.15 M (NH4)2SO4, 55 MG/ML PROTEIN, 4 DEG C, PH 6.15, HANGING DROP, MICROSEED FROM NATIVE FE-SOD OF P.SHERM., SOAKED FOR 24 H IN 150 MM SODIUM AZIDE, vapor diffusion - hanging drop - microseeding, temperature 277K	Resolution 1.55 Å R-free 0.198

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 1AVM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AR4 X-RAY STRUCTURE ANALYSIS OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN Deposited 1997-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Chain B 1–201（201 aa）	Not recorded	MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions microseeding；pH 6.1；277 K；PROTEIN WAS CRYSTALLIZED AT 50MG/ML FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15, 4 DEG C, NUCLEATION INDUCED BY MICROSEEDING FROM CRYSTALS GROWN FROM 14MG/ML PROTEIN, 2.4 M (NH4)2SO4, 50 MM KPI, PH 7.4, 4 DEG C., microseeding, temperature 277K	Resolution 1.90 Å R-free 0.205
1AR5 X-RAY STRUCTURE OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN Deposited 1997-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Chain B 1–201（201 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions microseeding；pH 6.15；277 K；PROTEIN WAS CRYSTALLIZED FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15 AT 4 DEG C. NUCLEATION WAS INDUCED BY ADDING A MICROSEED FROM CRYSTALS GROWN FROM 2.4 M (NH4)2SO4, 50MM KPI, PH 7.4 AT 4 DEG C., microseeding, temperature 277K	Resolution 1.60 Å R-free 0.184
1BS3 P.SHERMANII SOD(FE+3) FLUORIDE Deposited 1998-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Chain B 1–201（201 aa）	Not recorded	FE FE (III) ION × 4 F FLUORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；pH 6.1	Resolution 1.55 Å R-free 0.206
1BSM P.SHERMANII SOD(FE+3) 140K PH8 Deposited 1998-08-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Chain B 1–201（201 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；pH 8.1	Resolution 1.35 Å R-free 0.236
1BT8 P.SHERMANII SOD(FE+3) PH 10.0 Deposited 1998-09-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Chain B 1–201（201 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 10；pH 10.0	Resolution 1.85 Å R-free 0.236

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SODM_PROFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–201； UniProt 1–201 Author chain B； PDBConstruct 1–201； UniProt 1–201

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	1avm
Deposition date deposition_date	1997-09-17
Structure title title	THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE
Keywords keywords	OXIDOREDUCTASE, SOD, SUPEROXIDE DISMUTASE, PROPIONIBACTERIUM SHERMANII, AZIDE; 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	23.70 Å
Radius of gyration Rg (electron density) rg_electron	22.87 Å
Forward intensity I(0) i0	34601000.00
Molecular weight molecular_weight	45410.0 kDa
Excluded volume excluded_volume	56698 Å³
Envelope volume envelope_volume	67174 Å³
Hydration-shell volume shell_volume	24628 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	29.84 Å
Envelope Rg envelope_rg	23.17 Å
Shape Rg shape_rg	22.85 Å
Total Rg total_rg	23.77 Å
Total atoms total_atoms	3216
Residues n_residues	402
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	78.3 Å
Rg (real space) rg_real	23.66 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	3.4600e+07
I(0) uncertainty (real space) i0_real_error	4.3680e+05
Rg (reciprocal space) rg_reciprocal	23.67 Å
I(0) (reciprocal space) i0_reciprocal	34600000.0000
Solution quality estimate total_estimate	0.8938
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.368
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6985000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.999

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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	SUPEROXIDE DISMUTASE
Molecular weight formula_weight	22659.3 kDa
EC 编号 ec_number	1.15.1.1
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	3640

AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA

来源 Source

来源生物 organism	Propionibacterium freudenreichii subsp. shermanii
NCBI Class编号 ncbi_taxonomy_id	1752

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	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1avma1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1avma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d1avmb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1avmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1avmA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1avmA02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

Domain ID domain_id	1avmB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1avmB02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	79.680 Å
Unit-cell length b length_b	85.420 Å
Unit-cell length c length_c	108.760 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.1980

fit	/app/data/saxs_computation/av/1avm/1avm.fit
pddf	/app/data/pr_computation/av/1avm/1avm.pr.out
profile	/app/data/saxs_computation/av/1avm/1avm.dat

THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE

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