SAXSdb — 1dj2

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

ADENYLOSUCCINATE SYNTHETASE

Arabidopsis thaliana

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 48–490 Chain B； UniProt 48–490	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；PEG 4000, Lithium sulfate, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.90 Å R-free 0.273

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PURA_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–443； UniProt 48–490 Author chain B； PDBConstruct 1–443； UniProt 48–490

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	1dj2
Deposition date deposition_date	1999-12-01
Structure title title	STRUCTURES OF ADENYLOSUCCINATE SYNTHETASE FROM TRITICUM AESTIVUM AND ARABIDOPSIS THALIANA
Keywords keywords	GDP, LIGASE; LIGASE
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	28.03 Å
Radius of gyration Rg (electron density) rg_electron	27.01 Å
Forward intensity I(0) i0	141137000.00
Molecular weight molecular_weight	93903.0 kDa
Excluded volume excluded_volume	117600 Å³
Envelope volume envelope_volume	138890 Å³
Hydration-shell volume shell_volume	41020 Å³
Envelope diameter envelope_diameter	90.7 Å
Shell Rg shell_rg	35.90 Å
Envelope Rg envelope_rg	27.15 Å
Shape Rg shape_rg	27.02 Å
Total Rg total_rg	27.81 Å
Total atoms total_atoms	6612
Residues n_residues	858
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	86.1 Å
Rg (real space) rg_real	27.86 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.4110e+08
I(0) uncertainty (real space) i0_real_error	2.0030e+06
Rg (reciprocal space) rg_reciprocal	27.92 Å
I(0) (reciprocal space) i0_reciprocal	141100000.0000
Solution quality estimate total_estimate	0.9036
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-0.461
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94250000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.970

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	ADENYLOSUCCINATE SYNTHETASE
Molecular weight formula_weight	47886.2 kDa
EC 编号 ec_number	6.3.4.4
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	6612

SVAADSAATESLGRIGSLSQVSGVLGCQWGDEGKGKLVDILAQHFDIVARCQGGANAGHTIYNSEGKKFALHLVPSGILNEDTTCVIGNGVVVHLPGLFKEIDGLESNGVSCKGRILVSDRAHLLFDFHQEVDGLRESELAKSFIGTTKRGIGPAYSSKVIRNGIRVGDLRHMDTLPQKLDLLLSDAAARFQGFKYTPEMLREEVEAYKRYADRLEPYITDTVHFINDSISQKKKVLVEGGQATMLDIDFGTYPFVTSSSPSAGGICTGLGIAPSVVGDLIGVVKAYTTRVGSGPFPTENLGTGGDLLRLAGQEFGTTTGRPRRCGWLDIVALKFSCQINGFASLNLTKLDVLSDLNEIQLGVAYKRSDGTPVKSFPGDLRLLEELHVEYEVLPGWKSDISSVRNYSDLPKAAQQYVERIEELVGVPIHYIGIGPGRDALIYK

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dj2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d1dj2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (6 domains)

Domain ID domain_id	1dj2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	440 — Adenylosuccinate Synthetase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 1

Domain ID domain_id	1dj2A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	300 — Adenylosuccinate Synthetase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 2

Domain ID domain_id	1dj2A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	170 — Adenylosuccinate Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 3

Domain ID domain_id	1dj2B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	440 — Adenylosuccinate Synthetase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 1

Domain ID domain_id	1dj2B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	300 — Adenylosuccinate Synthetase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 2

Domain ID domain_id	1dj2B03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	170 — Adenylosuccinate Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Adenylosuccinate Synthetase, subunit A, domain 3

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8. Citations (1)

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Unit-cell length a length_a	212.760 Å
Unit-cell length b length_b	212.760 Å
Unit-cell length c length_c	212.760 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	48

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2730

fit	/app/data/saxs_computation/dj/1dj2/1dj2.fit
pddf	/app/data/pr_computation/dj/1dj2/1dj2.pr.out
profile	/app/data/saxs_computation/dj/1dj2/1dj2.dat

STRUCTURES OF ADENYLOSUCCINATE SYNTHETASE FROM TRITICUM AESTIVUM AND ARABIDOPSIS THALIANA

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

ADENYLOSUCCINATE SYNTHETASE

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