SAXSdb — 3eth

▼

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

Phosphoribosylaminoimidazole carboxylase ATPase subunit

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–355 Chain B； UniProt 1–355	Mutation：E61Q, Q205R	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% monomethylether poly(ethylene glycol) 5000, 10 mM MgATP, 10 mM aminopyrazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.228

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 3ETH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6R N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI Deposited 1999-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；100MM HEPPS, PH 7.8 0.575 M AMMONIUM SULFATE	Resolution 2.10 Å
1B6S STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE Deposited 1999-01-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa） Chain B 1–355（355 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å
1B6S STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE Deposited 1999-01-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–355（355 aa） Chain D 1–355（355 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å
3ETJ Crystal structure E. coli Purk in complex with Mg, ADP, and Pi Deposited 2008-10-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa） Chain B 1–355（355 aa）	Mutation：E61Q, Q205R Mutation：E61Q, Q205R	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 PI HYDROGENPHOSPHATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；monomethylether poly(ethylene glycol) 5000, MgATP, 5-aminoimidazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.215

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

View Construct and Data Evidence

UniProt name	PURK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain B； PDBConstruct 1–355； UniProt 1–355

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3eth
Deposition date deposition_date	2008-10-08
Structure title title	Crystal structure of E. coli Purk in complex with MgATP
Keywords keywords	ATP-grasp, purine biosynthesis, antimicrobial, ATP-binding, Decarboxylase, Lyase, Nucleotide-binding; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.52 Å
Radius of gyration Rg (electron density) rg_electron	28.98 Å
Forward intensity I(0) i0	104021000.00
Molecular weight molecular_weight	80074.0 kDa
Excluded volume excluded_volume	99911 Å³
Envelope volume envelope_volume	119030 Å³
Hydration-shell volume shell_volume	35317 Å³
Envelope diameter envelope_diameter	112.2 Å
Shell Rg shell_rg	35.13 Å
Envelope Rg envelope_rg	29.32 Å
Shape Rg shape_rg	28.99 Å
Total Rg total_rg	29.48 Å
Total atoms total_atoms	5638
Residues n_residues	710
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.4 Å
Rg (real space) rg_real	29.71 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.0400e+08
I(0) uncertainty (real space) i0_real_error	1.4900e+06
Rg (reciprocal space) rg_reciprocal	29.63 Å
I(0) (reciprocal space) i0_reciprocal	104000000.0000
Solution quality estimate total_estimate	0.8224
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.618
Kurtosis Kurtosis kurtosis	0.143
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38130000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.615; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.947

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Phosphoribosylaminoimidazole carboxylase ATPase subunit
Molecular weight formula_weight	39528.0 kDa
EC 编号 ec_number	4.1.1.21
Mutation mutation	E61Q, Q205R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6346

MKQVCVLGNGQLGRMLRQAGEPLGIAVWPVGLDAEPAAVPFQQSVITAEIERWPETALTRQLARHPAFVNRDVFPIIADRLTQKQLFDKLHLPTAPWQLLAERSEWPAVFDRLGELAIVKRRTGGYDGRGQWRLRANETEQLPAECYGECIVEQGINFSGEVSLVGARGFDGSTVFYPLTHNLHQDGILRTSVAFPQANAQQQARAEEMLSAIMQELGYVGVMAMECFVTPQGLLINELAPRVHNSGHWTQNGASISQFELHLRAITDLPLPQPVVNNPSVMINLIGSDVNYDWLKLPLVHLHWYDKEVRPGRKVGHLNLTDSDTSRLTATLEALIPLLPPEYASGVIWAQSKFG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	690

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3etha1
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.1 — BC C-terminal domain-like

Domain ID domain_id	d3etha2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.1 — BC N-terminal domain-like

Domain ID domain_id	d3etha3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.2 — BC ATP-binding domain-like

Domain ID domain_id	d3ethb1
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.1 — BC C-terminal domain-like

Domain ID domain_id	d3ethb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.1 — BC N-terminal domain-like

Domain ID domain_id	d3ethb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.2 — BC ATP-binding domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	3ethA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ethA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	3ethA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	3ethB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ethB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	3ethB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	57.101 Å
Unit-cell length b length_b	57.109 Å
Unit-cell length c length_c	59.215 Å
Unit-cell angle α angle_alpha	77.46 °
Unit-cell angle β angle_beta	82.39 °
Unit-cell angle γ angle_gamma	77.26 °
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	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1780
R_work r_work	0.1750
R_free r_free	0.2280

fit	/app/data/saxs_computation/et/3eth/3eth.fit
pddf	/app/data/pr_computation/et/3eth/3eth.pr.out
profile	/app/data/saxs_computation/et/3eth/3eth.dat

Crystal structure of E. coli Purk in complex with MgATP

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

Phosphoribosylaminoimidazole carboxylase ATPase subunit

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