SAXSdb — 1cyx

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

CYOA

Escherichia coli

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 111–315	Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315) Mutation：N172H, S207C, S209E, Y210I, S211C, F215H	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.316

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 1CYX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CYW QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA) Deposited 1995-08-22	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 111–315（205 aa） Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.326
1CYW QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA) Deposited 1995-08-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 111–315（205 aa） Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.326
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–315（315 aa）	Not recorded	CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–315（315 aa）	Not recorded	CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22	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 × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
7CUQ 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-24	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 × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
7CUW Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Deposited 2020-08-25	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 × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8F68 E. coli cytochrome bo3 ubiquinol oxidase monomer Deposited 2022-11-16	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 × 4 PDB declaration: tetrameric	Chain B 24–283（260 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8F6C E. coli cytochrome bo3 ubiquinol oxidase dimer Deposited 2022-11-16	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 × 8 PDB declaration: octameric	Chain B 24–283（260 aa） Chain F 24–283（260 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 HEO HEME O × 2 CU COPPER (II) ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8GO3 Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent Deposited 2022-08-24	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 × 4 PDB declaration: tetrameric	Chain B 1–315（315 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 UQ8 Ubiquinone-8 × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05	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 × 4 PDB declaration: tetrameric	Chain B 1–315（315 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCL, 150mM NaCl, 2% Glycerol, filtered and degassed. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYOA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 111–315

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	1cyx
Deposition date deposition_date	1995-08-22
Structure title title	QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERED CU-A BINDING SITE)(CYOA)
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	15.89 Å
Radius of gyration Rg (electron density) rg_electron	14.54 Å
Forward intensity I(0) i0	5714890.00
Molecular weight molecular_weight	17646.0 kDa
Excluded volume excluded_volume	22153 Å³
Envelope volume envelope_volume	24220 Å³
Hydration-shell volume shell_volume	13918 Å³
Envelope diameter envelope_diameter	46.7 Å
Shell Rg shell_rg	20.61 Å
Envelope Rg envelope_rg	14.75 Å
Shape Rg shape_rg	14.50 Å
Total Rg total_rg	15.80 Å
Total atoms total_atoms	1237
Residues n_residues	158
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	48.0 Å
Rg (real space) rg_real	15.75 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	5.7150e+06
I(0) uncertainty (real space) i0_real_error	5.9200e+04
Rg (reciprocal space) rg_reciprocal	15.77 Å
I(0) (reciprocal space) i0_reciprocal	5715000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.010
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	804200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.988

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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	CYOA
Molecular weight formula_weight	22742.7 kDa
EC 编号 ec_number	1.10.3.-
Mutation mutation	N172H, S207C, S209E, Y210I, S211C, F215H
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	1405

THALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMHSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGICAEICGPGHSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DINUCLEAR COPPER ION
Molecular weight formula_weight	127.1 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	168

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cyxa_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

CATH v4.4 (1 domains)

Domain ID domain_id	1cyxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (4)

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Unit-cell length a length_a	46.000 Å
Unit-cell length b length_b	98.200 Å
Unit-cell length c length_c	39.900 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	2.300 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.3160

fit	/app/data/saxs_computation/cy/1cyx/1cyx.fit
pddf	/app/data/pr_computation/cy/1cyx/1cyx.pr.out
profile	/app/data/saxs_computation/cy/1cyx/1cyx.dat

QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERED CU-A BINDING SITE)(CYOA)

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

CYOA

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