SAXSdb — 155c

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

CYTOCHROME C550

Paracoccus denitrificans

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 23–142	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 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.

Other PDB	Difference from Current Entry 155C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1COT X-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION Deposited 1994-07-06	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–149（129 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å

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

View Construct and Data Evidence

UniProt name	C550_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–122； UniProt 23–142

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	155c
Deposition date deposition_date	1976-08-01
Structure title title	THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550
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	15.28 Å
Radius of gyration Rg (electron density) rg_electron	13.86 Å
Forward intensity I(0) i0	4461320.00
Molecular weight molecular_weight	14509.0 kDa
Excluded volume excluded_volume	17923 Å³
Envelope volume envelope_volume	20234 Å³
Hydration-shell volume shell_volume	12307 Å³
Envelope diameter envelope_diameter	45.8 Å
Shell Rg shell_rg	19.69 Å
Envelope Rg envelope_rg	14.31 Å
Shape Rg shape_rg	13.83 Å
Total Rg total_rg	15.10 Å
Total atoms total_atoms	1017
Residues n_residues	134
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	47.4 Å
Rg (real space) rg_real	15.16 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	4.4610e+06
I(0) uncertainty (real space) i0_real_error	5.0880e+04
Rg (reciprocal space) rg_reciprocal	15.17 Å
I(0) (reciprocal space) i0_reciprocal	4461000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.086
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	660100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d155ca_
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	155cA00
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 (4)

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Unit-cell length a length_a	42.700 Å
Unit-cell length b length_b	82.170 Å
Unit-cell length c length_c	31.560 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Description description	CYTOCHROME C550
Molecular weight formula_weight	14275.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1017

THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550

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

CYTOCHROME C550

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Paracoccus denitrificans
通用名 common_name	Micrococcus denitrificans
NCBI Class编号 ncbi_taxonomy_id	266

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/55/155c/155c.fit
pddf	/app/data/pr_computation/55/155c/155c.pr.out
profile	/app/data/saxs_computation/55/155c/155c.dat