SAXSdb — 1coj

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

PROTEIN (SUPEROXIDE DISMUTASE)

Aquifex pyrophilus

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 2–212	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.90 Å R-free 0.200

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	SODF_AQUPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–212； UniProt 2–212

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	1coj
Deposition date deposition_date	1999-05-28
Structure title title	FE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM
Keywords keywords	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	19.88 Å
Radius of gyration Rg (electron density) rg_electron	18.65 Å
Forward intensity I(0) i0	10292100.00
Molecular weight molecular_weight	24305.0 kDa
Excluded volume excluded_volume	30566 Å³
Envelope volume envelope_volume	35675 Å³
Hydration-shell volume shell_volume	16583 Å³
Envelope diameter envelope_diameter	63.7 Å
Shell Rg shell_rg	24.40 Å
Envelope Rg envelope_rg	18.97 Å
Shape Rg shape_rg	18.63 Å
Total Rg total_rg	19.60 Å
Total atoms total_atoms	1717
Residues n_residues	211
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	63.2 Å
Rg (real space) rg_real	19.85 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.0290e+07
I(0) uncertainty (real space) i0_real_error	1.1700e+05
Rg (reciprocal space) rg_reciprocal	19.85 Å
I(0) (reciprocal space) i0_reciprocal	10290000.0000
Solution quality estimate total_estimate	0.8299
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.437
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1263000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (SUPEROXIDE DISMUTASE)
Molecular weight formula_weight	24376.6 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	1819

GVHKLEPKDHLKPQNLEGISNEQIEPHFEAHYKGYVAKYNEIQEKLADQNFADRSKANQNYSEYRELKVEETFNYMGVVLHELYFGMLTPGGKGEPSEALKKKIEEDIGGLDACTNELKAAAMAFRGWAILGLDIFSGRLVVNGLDAHNVYNLTGLIPLIVIDTYEHAYYVDYKNKRPPYIDAFFKNINWDVVNERFEKAMKAYEALKDFIK

来源 Source

来源生物 organism	Aquifex pyrophilus
NCBI Class编号 ncbi_taxonomy_id	2714
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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1coja1
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	d1coja2
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

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8. Citations (1)

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Unit-cell length a length_a	70.700 Å
Unit-cell length b length_b	75.630 Å
Unit-cell length c length_c	87.300 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	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.2000

fit	/app/data/saxs_computation/co/1coj/1coj.fit
pddf	/app/data/pr_computation/co/1coj/1coj.pr.out
profile	/app/data/saxs_computation/co/1coj/1coj.dat

FE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM

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

PROTEIN (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