SAXSdb — 5gyr

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

;Cytochrome c' ;

Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 24–154 Chain B； UniProt 24–154 Chain M； UniProt 24–154 Chain N； UniProt 24–154	Not recorded	HEC HEME C × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1mM sodium acetate, 0.2mM ammonium acetate, 30% (w/v) polyethylene glycol 3350	Resolution 1.60 Å R-free 0.232
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 24–154 Chain F； UniProt 24–154 Chain I； UniProt 24–154 Chain J； UniProt 24–154	Not recorded	HEC HEME C × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1mM sodium acetate, 0.2mM ammonium acetate, 30% (w/v) polyethylene glycol 3350	Resolution 1.60 Å R-free 0.232

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 5GYR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BBH ATOMIC STRUCTURE OF A CYTOCHROME C' WITH AN UNUSUAL LIGAND-CONTROLLED DIMER DISSOCIATION AT 1.8 ANGSTROMS RESOLUTION Deposited 1992-05-18	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 24–154（131 aa） Chain B 24–154（131 aa）	Not recorded	HEC HEME C × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å

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

View Construct and Data Evidence

UniProt name	CYCP_ALLVD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 24–154 Author chain B； PDBConstruct 1–131； UniProt 24–154 Author chain E； PDBConstruct 1–131； UniProt 24–154 Author chain F； PDBConstruct 1–131； UniProt 24–154 Author chain I； PDBConstruct 1–131； UniProt 24–154 Author chain J； PDBConstruct 1–131； UniProt 24–154 Author chain M； PDBConstruct 1–131； UniProt 24–154 Author chain N； PDBConstruct 1–131； UniProt 24–154

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	5gyr
Deposition date deposition_date	2016-09-23
Structure title title	Tetrameric Allochromatium vinosum cytochrome c'
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	34.07 Å
Radius of gyration Rg (electron density) rg_electron	33.35 Å
Forward intensity I(0) i0	219009000.00
Molecular weight molecular_weight	115250.0 kDa
Excluded volume excluded_volume	142690 Å³
Envelope volume envelope_volume	190100 Å³
Hydration-shell volume shell_volume	47335 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	40.25 Å
Envelope Rg envelope_rg	32.95 Å
Shape Rg shape_rg	33.35 Å
Total Rg total_rg	33.88 Å
Total atoms total_atoms	8080
Residues n_residues	1048
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	103.0 Å
Rg (real space) rg_real	33.93 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.1900e+08
I(0) uncertainty (real space) i0_real_error	3.1570e+06
Rg (reciprocal space) rg_reciprocal	34.02 Å
I(0) (reciprocal space) i0_reciprocal	219000000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	38850000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.782

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;Cytochrome c' ;
Molecular weight formula_weight	13806.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,J,M,N
Atom count atom_count	8888

AGLSPEEQIETRQAGYEFMGWNMGKIKANLEGEYNAAQVEAAANVIAAIANSGMGALYGPGTDKNVGDVKTRVKPEFFQNMEDVGKIAREFVGAANTLAEVAATGEAEAVKTAFGDVGAACKSCHEKYRAK

来源 Source

来源生物 organism	Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
NCBI Class编号 ncbi_taxonomy_id	572477
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	808

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5gyra_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyre_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrf_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyri_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrj_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrm_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrn_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

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8. Citations (1)

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Unit-cell length a length_a	82.949 Å
Unit-cell length b length_b	48.620 Å
Unit-cell length c length_c	130.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	41.400 Å
R factor r_factor	0.2055
R_work r_work	0.2041
R_free r_free	0.2323

fit	/app/data/saxs_computation/gy/5gyr/5gyr.fit
pddf	/app/data/pr_computation/gy/5gyr/5gyr.pr.out
profile	/app/data/saxs_computation/gy/5gyr/5gyr.dat

Tetrameric Allochromatium vinosum cytochrome c'

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

;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