SAXSdb — 1cyc

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

FERROCYTOCHROME C

Katsuwonus pelamis

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 1–103	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–103	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å

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	CYC_KATPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103

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	1cyc
Deposition date deposition_date	1976-08-01
Structure title title	THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION
Keywords keywords	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	19.94 Å
Radius of gyration Rg (electron density) rg_electron	19.21 Å
Forward intensity I(0) i0	9859240.00
Molecular weight molecular_weight	23845.0 kDa
Excluded volume excluded_volume	30071 Å³
Envelope volume envelope_volume	35787 Å³
Hydration-shell volume shell_volume	16256 Å³
Envelope diameter envelope_diameter	65.5 Å
Shell Rg shell_rg	24.38 Å
Envelope Rg envelope_rg	19.30 Å
Shape Rg shape_rg	19.18 Å
Total Rg total_rg	20.09 Å
Total atoms total_atoms	1676
Residues n_residues	206
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	66.2 Å
Rg (real space) rg_real	19.96 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	9.8590e+06
I(0) uncertainty (real space) i0_real_error	1.3590e+05
Rg (reciprocal space) rg_reciprocal	19.96 Å
I(0) (reciprocal space) i0_reciprocal	9859000.0000
Solution quality estimate total_estimate	0.8756
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.345
Kurtosis Kurtosis kurtosis	-0.480
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2613000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.970

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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	FERROCYTOCHROME C
Molecular weight formula_weight	11404.1 kDa
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	1677

GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS

来源 Source

来源生物 organism	Katsuwonus pelamis
通用名 common_name	skipjack tuna
NCBI Class编号 ncbi_taxonomy_id	8226

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cyca_
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

Domain ID domain_id	d1cycb_
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 (2 domains)

Domain ID domain_id	1cycA00
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

Domain ID domain_id	1cycB00
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

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8. Citations (7)

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Unit-cell length a length_a	57.680 Å
Unit-cell length b length_b	84.580 Å
Unit-cell length c length_c	37.830 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/cy/1cyc/1cyc.fit
pddf	/app/data/pr_computation/cy/1cyc/1cyc.pr.out
profile	/app/data/saxs_computation/cy/1cyc/1cyc.dat

THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION

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

FERROCYTOCHROME C

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