1c53

S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD

Method: X-RAY DIFFRACTION D_max: 37.8 Å Quality: GOOD

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

CYTOCHROME C553

;Desulfovibrio vulgaris str. 'Miyazaki F' ;

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 24–102	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 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	CY553_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 24–102

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c53
Deposition date deposition_date	1991-08-26
Structure title title	S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD
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	11.83 Å
Radius of gyration Rg (electron density) rg_electron	10.88 Å
Forward intensity I(0) i0	1652220.00
Molecular weight molecular_weight	9013.0 kDa
Excluded volume excluded_volume	10947 Å³
Envelope volume envelope_volume	6620 Å³
Hydration-shell volume shell_volume	6226 Å³
Envelope diameter envelope_diameter	31.9 Å
Shell Rg shell_rg	14.22 Å
Envelope Rg envelope_rg	9.92 Å
Shape Rg shape_rg	9.71 Å
Total Rg total_rg	11.73 Å
Total atoms total_atoms	43
Residues n_residues	—
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	37.8 Å
Rg (real space) rg_real	11.73 Å
Rg uncertainty (real space) rg_real_error	0.19 Å
I(0) (real space) i0_real	1.6520e+06
I(0) uncertainty (real space) i0_real_error	1.6040e+04
Rg (reciprocal space) rg_reciprocal	11.75 Å
I(0) (reciprocal space) i0_reciprocal	1652000.0000
Solution quality estimate total_estimate	0.7994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.020
Kurtosis Kurtosis kurtosis	-0.389
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	295400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c53a_
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

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8. Citations (3)

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Unit-cell length a length_a	42.700 Å
Unit-cell length b length_b	42.700 Å
Unit-cell length c length_c	103.400 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1940
R_work r_work	—
R_free r_free	—

Description description	CYTOCHROME C553
Molecular weight formula_weight	8411.7 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	122

S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD

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

CYTOCHROME C553

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) 1 domains

SCOP 2.08 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	;Desulfovibrio vulgaris str. 'Miyazaki F' ;
NCBI Class编号 ncbi_taxonomy_id	883

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/c5/1c53/1c53.fit
pddf	/app/data/pr_computation/c5/1c53/1c53.pr.out
profile	/app/data/saxs_computation/c5/1c53/1c53.dat