SAXSdb — 19hc

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

PROTEIN (NINE-HAEM CYTOCHROME C)

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 31–322 Chain B； UniProt 31–322	Not recorded	ACT ACETATE ION × 5 HEM PROTOPORPHYRIN IX CONTAINING FE × 18	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；PEG 6000 2-10% (W/V) SODIUM ACETATE BUFFER PH 5.5 0.25-0.75M	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.

Other PDB	Difference from Current Entry 19HC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OFW Three dimensional structure of the oxidized form of nine heme cytochrome c at PH 7.5 Deposited 2003-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–326（296 aa）	Not recorded	HEC HEME C × 9 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.50 Å R-free 0.207
1OFW Three dimensional structure of the oxidized form of nine heme cytochrome c at PH 7.5 Deposited 2003-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–326（296 aa）	Not recorded	HEC HEME C × 9 GOL GLYCEROL × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.50 Å R-free 0.207
1OFY three dimensional structure of the reduced form of nine-heme cytochrome c at ph 7.5 Deposited 2003-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–326（296 aa） Chain B 31–326（296 aa）	Not recorded	HEC HEME C × 18 ACT ACETATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.00 Å R-free 0.275

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC9_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 31–322 Author chain B； PDBConstruct 1–292； UniProt 31–322

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	19hc
Deposition date deposition_date	1998-12-01
Structure title title	NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
Keywords keywords	ELECTRON TRANSFER, 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	27.89 Å
Radius of gyration Rg (electron density) rg_electron	26.97 Å
Forward intensity I(0) i0	92196200.00
Molecular weight molecular_weight	73859.0 kDa
Excluded volume excluded_volume	91261 Å³
Envelope volume envelope_volume	110880 Å³
Hydration-shell volume shell_volume	33150 Å³
Envelope diameter envelope_diameter	92.1 Å
Shell Rg shell_rg	35.30 Å
Envelope Rg envelope_rg	26.96 Å
Shape Rg shape_rg	26.97 Å
Total Rg total_rg	27.81 Å
Total atoms total_atoms	5136
Residues n_residues	584
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	85.2 Å
Rg (real space) rg_real	27.75 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	9.2200e+07
I(0) uncertainty (real space) i0_real_error	1.2580e+06
Rg (reciprocal space) rg_reciprocal	27.80 Å
I(0) (reciprocal space) i0_reciprocal	92200000.0000
Solution quality estimate total_estimate	0.9138
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.118
Kurtosis Kurtosis kurtosis	-0.650
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29500000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.983

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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	PROTEIN (NINE-HAEM CYTOCHROME C)
Molecular weight formula_weight	31290.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6098

AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIADCETCHHTGDPVSCSTCHTVEGKAEGDYITLDRAMHATDIAARAKGNTPTSCVSCHQSETKERRECAGCHAITTPKDDEAWCATCHDITPSMTPSEMQKGIAGTLLPGDNEALAAETVLAEATVAPVSPMLAPYKVVIDALADKYEPSDFTHRRHLTSLMESIKDDKLAQAFHDKPEILCATCHHRSPLSLTPPKCGSCHTKEIDAADPGRPNLMAAYHLECMGCHKGMAVARPRDTDCTTCHKAAA

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

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	18

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	885

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d19hca_
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	d19hcb_
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 (4 domains)

Domain ID domain_id	19hcA01
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	19hcA02
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	19hcB01
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	19hcB02
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 (1)

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Unit-cell length a length_a	60.380 Å
Unit-cell length b length_b	106.070 Å
Unit-cell length c length_c	80.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	24.000 Å
R factor r_factor	0.1694
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/9h/19hc/19hc.fit
pddf	/app/data/pr_computation/9h/19hc/19hc.pr.out
profile	/app/data/saxs_computation/9h/19hc/19hc.dat

NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

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

PROTEIN (NINE-HAEM CYTOCHROME 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

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