SAXSdb — 1io3

▼

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

CYTOCHROME C2

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–127	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：Vapor diffusion, Sitting-drop and Soaking；pH 8.5；277 K；ammonium sulfate, Tris-HCl, potassium ferricyanide, pH 8.5, Vapor diffusion, Sitting-drop and Soaking , temperature 277.0K	Resolution 1.90 Å R-free 0.243

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 1IO3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CO6 CRYSTAL STRUCTURE OF FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS Deposited 1999-06-05	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–127（107 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；CRYSTALS WERE GROWN FROM AN AMMONIUM SULFATE SOLUTION AT PH 8.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å
1CRY APPLICATION OF AN AUTOMATIC MOLECULAR REPLACEMENT PROCEDURE TO CRYSTAL STRUCTURE OF CYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS Deposited 1993-12-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–127（107 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC2_RHOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 21–127

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1io3
Deposition date deposition_date	2001-01-06
Structure title title	CRYSTAL STRUCTURE OF FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS
Keywords keywords	HEME PROTEIN, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.16 Å
Radius of gyration Rg (electron density) rg_electron	12.63 Å
Forward intensity I(0) i0	3015330.00
Molecular weight molecular_weight	12272.0 kDa
Excluded volume excluded_volume	15408 Å³
Envelope volume envelope_volume	16346 Å³
Hydration-shell volume shell_volume	10975 Å³
Envelope diameter envelope_diameter	42.0 Å
Shell Rg shell_rg	18.43 Å
Envelope Rg envelope_rg	12.89 Å
Shape Rg shape_rg	12.61 Å
Total Rg total_rg	13.99 Å
Total atoms total_atoms	864
Residues n_residues	107
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	45.7 Å
Rg (real space) rg_real	14.04 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	3.0150e+06
I(0) uncertainty (real space) i0_real_error	2.7180e+04
Rg (reciprocal space) rg_reciprocal	14.05 Å
I(0) (reciprocal space) i0_reciprocal	3015000.0000
Solution quality estimate total_estimate	0.8828
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.060
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	448700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1io3a_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (1 domains)

Domain ID domain_id	1io3A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	75.970 Å
Unit-cell length b length_b	75.970 Å
Unit-cell length c length_c	40.370 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
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	0.2080
R_free r_free	0.2430

Description description	CYTOCHROME C2
Molecular weight formula_weight	11667.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	906

CRYSTAL STRUCTURE OF FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS

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

CYTOCHROME C2

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	42

fit	/app/data/saxs_computation/io/1io3/1io3.fit
pddf	/app/data/pr_computation/io/1io3/1io3.pr.out
profile	/app/data/saxs_computation/io/1io3/1io3.dat