SAXSdb — 3etj

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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	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

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 3ETJ	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
3ETH Crystal structure of E. coli Purk in complex with MgATP 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	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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3etj
Deposition date deposition_date	2008-10-08
Structure title title	Crystal structure E. coli Purk in complex with Mg, ADP, and Pi
Keywords keywords	ATP-grasp, purine biosynthesis, antimicrobial, ATP-binding, Decarboxylase, Lyase, Nucleotide-binding; LYASE
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	29.30 Å
Radius of gyration Rg (electron density) rg_electron	28.78 Å
Forward intensity I(0) i0	102704000.00
Molecular weight molecular_weight	79650.0 kDa
Excluded volume excluded_volume	99376 Å³
Envelope volume envelope_volume	118190 Å³
Hydration-shell volume shell_volume	35197 Å³
Envelope diameter envelope_diameter	111.6 Å
Shell Rg shell_rg	35.08 Å
Envelope Rg envelope_rg	29.14 Å
Shape Rg shape_rg	28.80 Å
Total Rg total_rg	29.27 Å
Total atoms total_atoms	5606
Residues n_residues	706
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	108.0 Å
Rg (real space) rg_real	29.47 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	1.0270e+08
I(0) uncertainty (real space) i0_real_error	1.5610e+06
Rg (reciprocal space) rg_reciprocal	29.40 Å
I(0) (reciprocal space) i0_reciprocal	102700000.0000
Solution quality estimate total_estimate	0.6328
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.0 Å
Skewness Skewness skewness	0.611
Kurtosis Kurtosis kurtosis	0.124
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41530000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.584; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 0.880; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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	6305

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'-DIPHOSPHATE
Molecular weight formula_weight	427.2 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 non-polymer

Description description	HYDROGENPHOSPHATE ION
Molecular weight formula_weight	96.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	681

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3etja1
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	d3etja2
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	d3etja3
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	d3etjb1
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	d3etjb2
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	d3etjb3
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	3etjA01
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	3etjA02
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	3etjA03
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	3etjB01
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	3etjB02
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	3etjB03
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

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8. Citations (1)

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Unit-cell length a length_a	128.800 Å
Unit-cell length b length_b	70.500 Å
Unit-cell length c length_c	88.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1600
R_work r_work	0.1580
R_free r_free	0.2150

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

Crystal structure E. coli Purk in complex with Mg, ADP, and Pi