1cxy

STRUCTURE AND CHARACTERIZATION OF ECTOTHIORHODOSPIRA VACUOLATA CYTOCHROME B558, A PROKARYOTIC HOMOLOGUE OF CYTOCHROME B5

Method: X-RAY DIFFRACTION D_max: 42.5 Å Quality: GOOD

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

CYTOCHROME B5

Ectothiorhodospira shaposhnikovii

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 1–90	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；MES, NACL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.220

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CYB5_ECTVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 1–90

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cxy
Deposition date deposition_date	1999-08-31
Structure title title	STRUCTURE AND CHARACTERIZATION OF ECTOTHIORHODOSPIRA VACUOLATA CYTOCHROME B558, A PROKARYOTIC HOMOLOGUE OF CYTOCHROME B5
Keywords keywords	HELIX, BETA-STRAND, 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	12.98 Å
Radius of gyration Rg (electron density) rg_electron	11.79 Å
Forward intensity I(0) i0	1865570.00
Molecular weight molecular_weight	9544.0 kDa
Excluded volume excluded_volume	11975 Å³
Envelope volume envelope_volume	12464 Å³
Hydration-shell volume shell_volume	9206 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	17.28 Å
Envelope Rg envelope_rg	12.15 Å
Shape Rg shape_rg	11.78 Å
Total Rg total_rg	13.15 Å
Total atoms total_atoms	672
Residues n_residues	81
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	42.5 Å
Rg (real space) rg_real	12.91 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.8660e+06
I(0) uncertainty (real space) i0_real_error	2.0380e+04
Rg (reciprocal space) rg_reciprocal	12.92 Å
I(0) (reciprocal space) i0_reciprocal	1866000.0000
Solution quality estimate total_estimate	0.8819
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-0.295
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	303100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.950

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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 B5
Molecular weight formula_weight	10106.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	848

NETEATLPVFTLEQVAEHHSPDDCWMAIHGKVYDLTPYVPNHPGPAGMMLVWCGQESTEAWETKSYGEPHSSLAARLLQRYLIGTLEEIT

来源 Source

来源生物 organism	Ectothiorhodospira shaposhnikovii
NCBI Class编号 ncbi_taxonomy_id	1054
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	166

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cxya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

CATH v4.4 (1 domains)

Domain ID domain_id	1cxyA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

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8. Citations (1)

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Unit-cell length a length_a	46.406 Å
Unit-cell length b length_b	46.406 Å
Unit-cell length c length_c	91.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1860
R_work r_work	0.1990
R_free r_free	0.2200

fit	/app/data/saxs_computation/cx/1cxy/1cxy.fit
pddf	/app/data/pr_computation/cx/1cxy/1cxy.pr.out
profile	/app/data/saxs_computation/cx/1cxy/1cxy.dat