SAXSdb — 2cxb

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

CYTOCHROME C2

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 22–145	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.95 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–145	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.95 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 2CXB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CXA CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS Deposited 1994-02-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–145（124 aa）	Not recorded	IMD IMIDAZOLE × 1 HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1CXC CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS Deposited 1994-02-14	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–145（124 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1L9B X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type II Co-Crystals Deposited 2002-03-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 22–145（124 aa）	Not recorded	NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.40 Å R-free 0.264
1L9J X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals Deposited 2002-03-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 22–145（124 aa）	Not recorded	BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.25 Å R-free 0.287
1L9J X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals Deposited 2002-03-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 22–145（124 aa）	Not recorded	BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.25 Å R-free 0.287

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

View Construct and Data Evidence

UniProt name	CYC2_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 22–145 Author chain B； PDBConstruct 1–124； UniProt 22–145

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	2cxb
Deposition date deposition_date	1994-04-21
Structure title title	CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS
Keywords keywords	ELECTRON TRANSPORT (CYTOCHROME); ELECTRON TRANSPORT (CYTOCHROME)
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	23.16 Å
Radius of gyration Rg (electron density) rg_electron	22.59 Å
Forward intensity I(0) i0	13452700.00
Molecular weight molecular_weight	27298.0 kDa
Excluded volume excluded_volume	33857 Å³
Envelope volume envelope_volume	41387 Å³
Hydration-shell volume shell_volume	16280 Å³
Envelope diameter envelope_diameter	82.6 Å
Shell Rg shell_rg	27.73 Å
Envelope Rg envelope_rg	22.49 Å
Shape Rg shape_rg	22.57 Å
Total Rg total_rg	23.31 Å
Total atoms total_atoms	1924
Residues n_residues	246
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	77.3 Å
Rg (real space) rg_real	23.31 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.3450e+07
I(0) uncertainty (real space) i0_real_error	2.0830e+05
Rg (reciprocal space) rg_reciprocal	23.28 Å
I(0) (reciprocal space) i0_reciprocal	13450000.0000
Solution quality estimate total_estimate	0.7560
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.417
Kurtosis Kurtosis kurtosis	-0.575
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4137000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.728; 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2cxba_
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

Domain ID domain_id	d2cxbb_
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 (2 domains)

Domain ID domain_id	2cxbA00
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

Domain ID domain_id	2cxbB00
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	45.310 Å
Unit-cell length b length_b	37.970 Å
Unit-cell length c length_c	37.600 Å
Unit-cell angle α angle_alpha	102.94 °
Unit-cell angle β angle_beta	72.44 °
Unit-cell angle γ angle_gamma	90.57 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1720
R_work r_work	—
R_free r_free	—

Description description	CYTOCHROME C2
Molecular weight formula_weight	13488.1 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	2128

CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS

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

CYTOCHROME C2

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

fit	/app/data/saxs_computation/cx/2cxb/2cxb.fit
pddf	/app/data/pr_computation/cx/2cxb/2cxb.pr.out
profile	/app/data/saxs_computation/cx/2cxb/2cxb.dat