SAXSdb — 1czj

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

CYTOCHROME C3

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–111	Not recorded	SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；THE CRYSTALS WERE GROWN AT 20 DEGREES C. DATA WAS COLLECTED AT AT 4 DEGREES C., pH 8.0	Resolution 2.16 Å R-free 0.263

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 1CZJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AQE CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III (AMBLER) 26 KD Deposited 1997-07-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–111（111 aa）	Mutation：Y73E	SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；THE PROTEIN WAS CRYSTALLIZED FROM 2.4M AMMONIUM SULFATE, 100MM TRIS PH 7.6	Resolution 2.20 Å R-free 0.239

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC32_DESDN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 1–111

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	1czj
Deposition date deposition_date	1996-01-12
Structure title title	CYTOCHROME C OF CLASS III (AMBLER) 26 KD
Keywords keywords	OCTAHEME CYTOCHROME, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	15.02 Å
Radius of gyration Rg (electron density) rg_electron	13.86 Å
Forward intensity I(0) i0	4863060.00
Molecular weight molecular_weight	14951.0 kDa
Excluded volume excluded_volume	18258 Å³
Envelope volume envelope_volume	20429 Å³
Hydration-shell volume shell_volume	12391 Å³
Envelope diameter envelope_diameter	47.3 Å
Shell Rg shell_rg	19.81 Å
Envelope Rg envelope_rg	14.42 Å
Shape Rg shape_rg	13.85 Å
Total Rg total_rg	15.05 Å
Total atoms total_atoms	1039
Residues n_residues	110
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	48.0 Å
Rg (real space) rg_real	14.92 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	4.8630e+06
I(0) uncertainty (real space) i0_real_error	4.9320e+04
Rg (reciprocal space) rg_reciprocal	14.93 Å
I(0) (reciprocal space) i0_reciprocal	4863000.0000
Solution quality estimate total_estimate	0.8848
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.4 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	992600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.954

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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	CYTOCHROME C3
Molecular weight formula_weight	12541.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1105

ETFEIPESVTMSPKQFEGYTPKKGDVTFNHASHMDIACQQCHHTVPDTYTIESCMTEGCHDNIKERTEISSVYRTFHTTKDSEKSCVGCHRELKRQGPSDAPLACNSCHVQ

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1czja_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.1 — Cytochrome c3-like

CATH v4.4 (1 domains)

Domain ID domain_id	1czjA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	10 — Cytochrome C3
Homologous superfamily homologous superfamily	10 — Cytochrome C3

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8. Citations (2)

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Unit-cell length a length_a	73.710 Å
Unit-cell length b length_b	73.710 Å
Unit-cell length c length_c	57.250 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2630

fit	/app/data/saxs_computation/cz/1czj/1czj.fit
pddf	/app/data/pr_computation/cz/1czj/1czj.pr.out
profile	/app/data/saxs_computation/cz/1czj/1czj.dat

CYTOCHROME C OF CLASS III (AMBLER) 26 KD

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

CYTOCHROME C3

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