SAXSdb — 1c6r

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

CYTOCHROME C6

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 1–89	Not recorded	CD CADMIUM ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50	Resolution 1.90 Å R-free 0.260

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 1C6R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C6O CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS Deposited 1999-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa） Chain B 1–89（89 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.00 Å R-free 0.279

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

View Construct and Data Evidence

UniProt name	CYC6_SCEOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 1–89

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	1c6r
Deposition date deposition_date	1999-04-06
Structure title title	CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS
Keywords keywords	ELECTRON TRANSPORT PROTEIN, CYTOCHROME-C6, REDUCED STATE, PHOTOSYNTHESIS, 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	13.25 Å
Radius of gyration Rg (electron density) rg_electron	11.70 Å
Forward intensity I(0) i0	2624810.00
Molecular weight molecular_weight	10380.0 kDa
Excluded volume excluded_volume	12396 Å³
Envelope volume envelope_volume	12982 Å³
Hydration-shell volume shell_volume	9602 Å³
Envelope diameter envelope_diameter	37.0 Å
Shell Rg shell_rg	17.25 Å
Envelope Rg envelope_rg	11.78 Å
Shape Rg shape_rg	11.52 Å
Total Rg total_rg	13.29 Å
Total atoms total_atoms	702
Residues n_residues	88
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	38.8 Å
Rg (real space) rg_real	13.14 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	2.6250e+06
I(0) uncertainty (real space) i0_real_error	2.6430e+04
Rg (reciprocal space) rg_reciprocal	13.14 Å
I(0) (reciprocal space) i0_reciprocal	2625000.0000
Solution quality estimate total_estimate	0.9088
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.037
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	319200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.985

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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	CYTOCHROME C6
Molecular weight formula_weight	9415.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	769

SADLALGKQTFEANCAACHAGGNNSVIPDHTLRKAAMEQFLQGGFNLEAITYQVENGKGAMPAWSGTLDDDEIAAVAAYVYDQASGDKW

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c6ra_
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	1c6rA00
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 (1)

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Unit-cell length a length_a	35.560 Å
Unit-cell length b length_b	48.470 Å
Unit-cell length c length_c	43.920 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1995
R_free r_free	0.2600

fit	/app/data/saxs_computation/c6/1c6r/1c6r.fit
pddf	/app/data/pr_computation/c6/1c6r/1c6r.pr.out
profile	/app/data/saxs_computation/c6/1c6r/1c6r.dat

CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS

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

CYTOCHROME C6

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