SAXSdb — 2b4z

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

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–104	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROSEEDING；pH 7；277 K；PEG 1000, SODIUM PHOSPHATE, pH 7.0, MICROSEEDING, temperature 277K	Resolution 1.50 Å R-free 0.218

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 2B4Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YBB Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876) Deposited 2011-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain Y 2–105（104 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 MG MAGNESIUM ION × 7 FES FE2/S2 (INORGANIC) CLUSTER × 4 CA CALCIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 5 SMA STIGMATELLIN A × 2 UQ1 UBIQUINONE-1 × 2 HEC HEME C × 2 CDL CARDIOLIPIN × 4 HEA HEME-A × 2 CU COPPER (II) ION × 3 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE；pH 7.7；10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE WAS ADSORBED TO CARBON FILM FOR 30 SECONDS BEFORE BLOTTING	Resolution 19.00 Å
3J2T An improved model of the human apoptosome Deposited 2012-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 2–105（104 aa） Chain I 2–105（104 aa） Chain J 2–105（104 aa） Chain K 2–105（104 aa） Chain L 2–105（104 aa） Chain M 2–105（104 aa） Chain N 2–105（104 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer low salt HEPES buffer；pH 7.5；20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT cryo-EM vitrification conditions Blot for 2 seconds before plunging；77 K；Cryogen ETHANE；Blot for 2 seconds before plunging (FEI VITROBOT MARK III)	Resolution 9.50 Å
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain H 2–105（104 aa） Chain I 2–105（104 aa） Chain J 2–105（104 aa） Chain K 2–105（104 aa） Chain L 2–105（104 aa） Chain M 2–105（104 aa） Chain N 2–105（104 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 HEC HEME C × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer A cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6FF5 X-ray structure of bovine heart cytochrome c at high ionic strength Deposited 2018-01-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–105（104 aa）	Not recorded	HEC HEME C × 1 NO3 NITRATE ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.2-3.4 M ammonium sulfate and 0.4-0.5 M NaNO3	Resolution 1.74 Å R-free 0.203

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104

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	2b4z
Deposition date deposition_date	2005-09-27
Structure title title	Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.
Keywords keywords	FERRIC FORM, LOW IONIC STRENGTH, 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	13.99 Å
Radius of gyration Rg (electron density) rg_electron	12.56 Å
Forward intensity I(0) i0	2953600.00
Molecular weight molecular_weight	12197.0 kDa
Excluded volume excluded_volume	15400 Å³
Envelope volume envelope_volume	16368 Å³
Hydration-shell volume shell_volume	10971 Å³
Envelope diameter envelope_diameter	42.0 Å
Shell Rg shell_rg	18.52 Å
Envelope Rg envelope_rg	12.95 Å
Shape Rg shape_rg	12.51 Å
Total Rg total_rg	14.08 Å
Total atoms total_atoms	857
Residues n_residues	104
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	46.3 Å
Rg (real space) rg_real	13.88 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.9540e+06
I(0) uncertainty (real space) i0_real_error	3.1830e+04
Rg (reciprocal space) rg_reciprocal	13.89 Å
I(0) (reciprocal space) i0_reciprocal	2954000.0000
Solution quality estimate total_estimate	0.7923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.098
Kurtosis Kurtosis kurtosis	-0.310
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	566100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2b4za_
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	2b4zA00
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	36.840 Å
Unit-cell length b length_b	54.480 Å
Unit-cell length c length_c	55.330 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.520 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2180

Description description	Cytochrome c
Molecular weight formula_weight	11595.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1079

Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.

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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

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	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

fit	/app/data/saxs_computation/b4/2b4z/2b4z.fit
pddf	/app/data/pr_computation/b4/2b4z/2b4z.pr.out
profile	/app/data/saxs_computation/b4/2b4z/2b4z.dat