SAXSdb — 2p1x

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

Protein cyaY

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 1–106	Not recorded	EU3 EUROPIUM (III) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；Crystallization conditions: protein concentration 15mg/ml, 0.1M sodium acetate, 0.2M CaCl2, 30% PEG 4000, 2mM beta mercaptoethanol Soaking conditions: EuCl3 in the stabilizing solution, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.42 Å R-free 0.222

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 2P1X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EW4 CRYSTAL STRUCTURE OF ESCHERICHIA COLI CYAY PROTEIN REVEALS A NOVEL FOLD FOR THE FRATAXIN FAMILY Deposited 2000-04-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.12；296 K；0.1 M sodium acetate, 34% PEG 4000, pH 5.12, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.40 Å R-free 0.213
1SOY Solution structure of the bacterial frataxin orthologue, CyaY Deposited 2004-03-16	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM KCl；Pressure ambient NMR sample composition 0.5mM CyaY U-15N,13C, 50mM Phosphate buffer, 150mM KCl, 1mM DTT, 0.05%NaN3 \| 90% H2O/10% D2O NMR sample composition 0.5mM CyaY 15N, 50mM Phosphate buffer, 150mM KCl, 1mM DTT, 0.05%NaN3 \| 90% H2O/10% D2O	Resolution not provided
2EFF Crystal structure analysis of the complex between CyaY and Co(II) Deposited 2007-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；30% w/v PEG 4000, 200mM CoCl2, 2mM beta-mercaptoethanol, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.228

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYAY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 1–106

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	2p1x
Deposition date deposition_date	2007-03-06
Structure title title	Crystal structure analysis of the complex between CyaY and Eu(III)
Keywords keywords	;FRATAXIN, FRIEDREICH'S ATAXIA IRON BINDING, IRON-SULFUR CLUSTER ASSEMBLY, DETOXIFYING REDOX-ACTIVE IRON, UNKNOWN FUNCTION ;; UNKNOWN FUNCTION
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	15.42 Å
Radius of gyration Rg (electron density) rg_electron	13.65 Å
Forward intensity I(0) i0	4147150.00
Molecular weight molecular_weight	12913.0 kDa
Excluded volume excluded_volume	15203 Å³
Envelope volume envelope_volume	17201 Å³
Hydration-shell volume shell_volume	11099 Å³
Envelope diameter envelope_diameter	49.6 Å
Shell Rg shell_rg	18.86 Å
Envelope Rg envelope_rg	13.72 Å
Shape Rg shape_rg	13.38 Å
Total Rg total_rg	15.25 Å
Total atoms total_atoms	865
Residues n_residues	106
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	49.8 Å
Rg (real space) rg_real	15.34 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	4.1470e+06
I(0) uncertainty (real space) i0_real_error	4.2370e+04
Rg (reciprocal space) rg_reciprocal	15.35 Å
I(0) (reciprocal space) i0_reciprocal	4147000.0000
Solution quality estimate total_estimate	0.8903
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	331500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.993

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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	Protein cyaY
Molecular weight formula_weight	12242.4 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	978

MNDSEFHRLADQLWLTIEERLDDWDGDSDIDCEINGGVLTITFENGSKIIINRQEPLHQVWLATKQGGYHFDLKGDEWICDRSGETFWDLLEQAATQQAGETVSFR

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	EUROPIUM (III) ION
Molecular weight formula_weight	152.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2p1xa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamily	d.82.2 — Frataxin/Nqo15-like
Family Family family	d.82.2.1 — Frataxin-like

CATH v4.4 (1 domains)

Domain ID domain_id	2p1xA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	920 — Metal Transport, Frataxin; Chain A
Homologous superfamily homologous superfamily	10 — Frataxin/CyaY

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8. Citations (3)

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Unit-cell length a length_a	43.859 Å
Unit-cell length b length_b	43.859 Å
Unit-cell length c length_c	98.717 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	1.420 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2010
R_work r_work	0.1990
R_free r_free	0.2220

fit	/app/data/saxs_computation/p1/2p1x/2p1x.fit
pddf	/app/data/pr_computation/p1/2p1x/2p1x.pr.out
profile	/app/data/saxs_computation/p1/2p1x/2p1x.dat

Crystal structure analysis of the complex between CyaY and Eu(III)

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

Protein cyaY

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