SAXSdb — 2cth

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 23–129	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)	Resolution 1.67 Å R-free 0.190
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 23–129	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)	Resolution 1.67 Å R-free 0.190

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 2CTH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A2I SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES Deposited 1998-01-05	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–129（107 aa）	Not recorded	HEC HEME C × 4	SOLUTION NMR NMR measurement conditions pH 8.5；303 K	Resolution not provided
1GX7 Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase Deposited 2002-03-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 23–129（107 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4	Experimental method not declared NMR measurement conditions pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1	Resolution not provided
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–129（107 aa）	Mutation：F20L	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–129（107 aa）	Mutation：F20L	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 23–129（107 aa） Chain B 23–129（107 aa）	Mutation：F20L Mutation：F20L	HEM PROTOPORPHYRIN IX CONTAINING FE × 32	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.30 Å R-free 0.296
2BPN SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES Deposited 2005-04-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–129（107 aa） Fragment：CYTOCHROME C3, RESIDUES 23-129	Not recorded	HEC HEME C × 4	SOLUTION NMR NMR measurement conditions pH 7.1；303 K NMR sample composition 92% WATER/8% D2O AND 100% D2O	Resolution not provided
2CYM EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION Deposited 1993-09-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–129（107 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC3_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 23–129 Author chain B； PDBConstruct 1–107； UniProt 23–129

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	2cth
Deposition date deposition_date	1997-06-18
Structure title title	CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
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	22.71 Å
Radius of gyration Rg (electron density) rg_electron	22.46 Å
Forward intensity I(0) i0	14660300.00
Molecular weight molecular_weight	28263.0 kDa
Excluded volume excluded_volume	34933 Å³
Envelope volume envelope_volume	42548 Å³
Hydration-shell volume shell_volume	17064 Å³
Envelope diameter envelope_diameter	78.9 Å
Shell Rg shell_rg	27.40 Å
Envelope Rg envelope_rg	22.61 Å
Shape Rg shape_rg	22.43 Å
Total Rg total_rg	23.18 Å
Total atoms total_atoms	1964
Residues n_residues	214
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	78.3 Å
Rg (real space) rg_real	22.93 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.4660e+07
I(0) uncertainty (real space) i0_real_error	2.1320e+05
Rg (reciprocal space) rg_reciprocal	22.88 Å
I(0) (reciprocal space) i0_reciprocal	14660000.0000
Solution quality estimate total_estimate	0.8041
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.519
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4942000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.607; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.639; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ctha_
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

Domain ID domain_id	d2cthb_
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 (2 domains)

Domain ID domain_id	2cthA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	10 — Cytochrome C3
Homologous superfamily homologous superfamily	10 — Cytochrome C3

Domain ID domain_id	2cthB00
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	77.300 Å
Unit-cell length b length_b	77.300 Å
Unit-cell length c length_c	77.100 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1530
R_work r_work	—
R_free r_free	0.1900

Description description	CYTOCHROME C3
Molecular weight formula_weight	11687.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2088

CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH

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

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	8

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

fit	/app/data/saxs_computation/ct/2cth/2cth.fit
pddf	/app/data/pr_computation/ct/2cth/2cth.pr.out
profile	/app/data/saxs_computation/ct/2cth/2cth.dat