SAXSdb — 1a48

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

PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE

OrganismNot specified

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 2–306	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

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 1A48	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OBD SAICAR-synthase complexed with ATP Deposited 2003-01-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–306（305 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE HANGING DROPS CONTAINED PROTEIN AT A CONCENTRATION OF 8 - 15 MG/ML, 50 MM TRIS-HCL BUFFER, PH 7.0, 40 MM ASPARTIC ACID AND 1.0 - 1.25 M AMMONIUM SULPHATE. THE WELL CONTAINED THE SAME ABOVE BUFFER PLUS 2.25 M AMMONIUM SULPHATE	Resolution 1.40 Å R-free 0.195
1OBG SAICAR-synthase complexed with ATP Deposited 2003-01-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–306（305 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；40MM ASP. ASID, 10MM MGCL2, 25MM ATP, 2.26 M (NH4)2(SO4), 5, pH 4.50	Resolution 2.05 Å R-free 0.206
2CNQ Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate Deposited 2006-05-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–306（305 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 2 AMZ AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE × 2 AMP ADENOSINE MONOPHOSPHATE × 1 SIN SUCCINIC ACID × 2 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SUPHATE, ATP, AICAR, MG, ASP, pH 7.50	Resolution 1.00 Å R-free 0.130
2CNU Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–306（305 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ASP ASPARTIC ACID × 3 SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE	Resolution 1.05 Å R-free 0.159
2CNV SAICAR-synthase from Saccharomyces cerevisiae complexed SAICAR Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–306（305 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ASP ASPARTIC ACID × 2 SSS N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, ASPARTIC ACID, TRIS-HCL BUFFER, pH 7.50	Resolution 2.00 Å R-free 0.238

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUR7_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–306； UniProt 2–306

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	1a48
Deposition date deposition_date	1998-02-12
Structure title title	SAICAR SYNTHASE
Keywords keywords	ATP BINDING PROTEIN, PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYNTHASE, PURINE BIOSYNTHESIS; ATP BINDING PROTEIN
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	20.77 Å
Radius of gyration Rg (electron density) rg_electron	19.79 Å
Forward intensity I(0) i0	18994500.00
Molecular weight molecular_weight	33906.0 kDa
Excluded volume excluded_volume	42867 Å³
Envelope volume envelope_volume	50658 Å³
Hydration-shell volume shell_volume	21262 Å³
Envelope diameter envelope_diameter	70.7 Å
Shell Rg shell_rg	26.23 Å
Envelope Rg envelope_rg	19.89 Å
Shape Rg shape_rg	19.78 Å
Total Rg total_rg	20.75 Å
Total atoms total_atoms	2393
Residues n_residues	298
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	79.9 Å
Rg (real space) rg_real	20.65 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.8990e+07
I(0) uncertainty (real space) i0_real_error	2.5570e+05
Rg (reciprocal space) rg_reciprocal	20.67 Å
I(0) (reciprocal space) i0_reciprocal	18990000.0000
Solution quality estimate total_estimate	0.7299
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.170
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6142000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.518; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.000

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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	PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
Molecular weight formula_weight	34545.2 kDa
EC 编号 ec_number	6.3.2.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2721

XSITKTELDGILPLVARGKVRDIYEVDAGTLLFVATDRISAYDVIMENSIPEKGILLTKLSEFWFKFLSNDVRNHLVDIAPGKTIFDYLPAKLSEPKYKTQLEDRSLLVHKHKLIPLEVIVRGYITGSAWKEYVKTGTVHGLKQPQGLKESQEFPEPIFTPSTKAEQGEHDENISPAQAAELVGEDLSRRVAELAVKLYSKCKDYAKEKGIIIADTKFEFGIDEKTNEIILVDEVLTPDSSRFWNGASYKVGESQDSYDKQFLRDWLTANKLNGVNGVKMPQDIVDRTRAKYIEAYETLTGSKWSH

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a48a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.143 — SAICAR synthase-like
Superfamily Superfamily superfamily	d.143.1 — SAICAR synthase-like
Family Family family	d.143.1.1 — SAICAR synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1a48A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1a48A02
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

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8. Citations (7)

The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.

Structure (1998)

PMID: 9551557 · DOI: 10.1016/S0969-2126(98)00038-0 PRIMARY

;[Substrate Specificity of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide Synthetase (Saicar-Synthetase) from Saccharomyces Cerevisiae Yeast] (Russian) ;

Biokhimiia (1992)

;Crystallization and Preliminary X-Ray Investigation of Phosphoribosylaminoimidazolesuccinocarboxamide Synthase from the Yeast Saccharomyces Cerevisiae ;

J.Mol.Biol. (1992)

De Novo Purine Nucleotide Biosynthesis

Prog.Nucleic Acid Res.Mol.Biol. (1992)

The Saccharomyces Cerevisiae Ade1 Gene: Structure, Overexpression and Possible Regulation by General Amino Acid Control

Gene (1991)

;[Isolation and Properties of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide-Synthetase from Saccharomyces Cerevisiae Yeasts] (Russian) ;

Biokhimiia (1989)

[Nucleotide Sequence of the Ade 1 Gene of the Yeast Saccharomyces Cerevisiae] (Russian)

Bioorg.Khim. (1986)

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Unit-cell length a length_a	62.600 Å
Unit-cell length b length_b	63.700 Å
Unit-cell length c length_c	81.200 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	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1530
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/a4/1a48/1a48.fit
pddf	/app/data/pr_computation/a4/1a48/1a48.pr.out
profile	/app/data/saxs_computation/a4/1a48/1a48.dat

SAICAR SYNTHASE

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

PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE

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