SAXSdb — 3pga

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

GLUTAMINASE-ASPARAGINASE

Pseudomonas sp. 7A

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain 1； UniProt 8–337 Chain 2； UniProt 8–337 Chain 3； UniProt 8–337 Chain 4； UniProt 8–337	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 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 3PGA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJO Crystal structure of Pseudomonas 7A Glutaminase-asparaginase with the inhibitor donv covalently bound in the active site Deposited 1999-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 8–337（330 aa） Chain B 8–337（330 aa）	Not recorded	CAB 4,4-dihydroxy-5-oxo-L-norvaline × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.238
1DJP CRYSTAL STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH THE INHIBITOR DON COVALENTLY BOUND IN THE ACTIVE SITE Deposited 1999-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 8–337（330 aa） Chain B 8–337（330 aa）	Not recorded	DO2 5,5-dihydroxy-6-oxo-L-norleucine × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.228
4PGA GLUTAMINASE-ASPARAGINASE FROM PSEUDOMONAS 7A Deposited 1997-01-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	SO4 SULFATE ION × 4 NH4 AMMONIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.70 Å R-free 0.254

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

View Construct and Data Evidence

UniProt name	ASPQ_PSES7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 8–337； UniProt 8–337 Author chain 2； PDBConstruct 8–337； UniProt 8–337 Author chain 3； PDBConstruct 8–337； UniProt 8–337 Author chain 4； PDBConstruct 8–337； UniProt 8–337

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	3pga
Deposition date deposition_date	1994-07-19
Structure title title	STRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE
Keywords keywords	BACTERIAL AMIDOHYDROLASE; BACTERIAL AMIDOHYDROLASE
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	30.75 Å
Radius of gyration Rg (electron density) rg_electron	29.65 Å
Forward intensity I(0) i0	286858000.00
Molecular weight molecular_weight	134030.0 kDa
Excluded volume excluded_volume	167580 Å³
Envelope volume envelope_volume	197380 Å³
Hydration-shell volume shell_volume	51812 Å³
Envelope diameter envelope_diameter	91.0 Å
Shell Rg shell_rg	39.52 Å
Envelope Rg envelope_rg	29.70 Å
Shape Rg shape_rg	29.62 Å
Total Rg total_rg	30.59 Å
Total atoms total_atoms	9424
Residues n_residues	1238
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	89.0 Å
Rg (real space) rg_real	30.50 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	2.8690e+08
I(0) uncertainty (real space) i0_real_error	4.0550e+06
Rg (reciprocal space) rg_reciprocal	30.61 Å
I(0) (reciprocal space) i0_reciprocal	286900000.0000
Solution quality estimate total_estimate	0.9030
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.058
Kurtosis Kurtosis kurtosis	-0.571
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	181600000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3pga1_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
Family Family family	c.88.1.1 — Glutaminase/Asparaginase

Domain ID domain_id	d3pga2_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
Family Family family	c.88.1.1 — Glutaminase/Asparaginase

Domain ID domain_id	d3pga3_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
Family Family family	c.88.1.1 — Glutaminase/Asparaginase

Domain ID domain_id	d3pga4_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
Family Family family	c.88.1.1 — Glutaminase/Asparaginase

CATH v4.4 (8 domains)

Domain ID domain_id	3pga101
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1170 — L-asparaginase, N-terminal domain

Domain ID domain_id	3pga102
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3pga201
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1170 — L-asparaginase, N-terminal domain

Domain ID domain_id	3pga202
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3pga301
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1170 — L-asparaginase, N-terminal domain

Domain ID domain_id	3pga302
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3pga401
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1170 — L-asparaginase, N-terminal domain

Domain ID domain_id	3pga402
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	40 —

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8. Citations (7)

Structural characterization of Pseudomonas 7A glutaminase-asparaginase.

Biochemistry (1994)

PMID: 8068664 · DOI: 10.1021/bi00200a005 PRIMARY

;A Left-Handed Crossover Involved in Amidohydrolase Catalysis: Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate ;

FEBS Lett. (1993)

Crystal Structure of E. Coli L-Asparaginase, an Enzyme Used in Cancer Therapy

Proc.Natl.Acad.Sci.USA (1993)

The Molecular Symmetry of Glutaminase-Asparaginases: Rotation Function Studies of the Pseudomonas 7A and Acinetobacter Enzymes

Acta Crystallogr.,Sect.B (1983)

Amino Acid Sequence of the Diazooxonorleucine Binding Site of Acinetobacter and Pseudomonas 7A Glutaminase-Asparaginase Enzymes

Biochemistry (1978)

Characterization of Crystals of L-Glutaminase-Asparaginase from Acinetobacter Glutaminasificans and Pseudomonas 7A

J.Mol.Biol. (1977)

Refined Crystal Structure of Acinetobacter Glutaminasificans Glutaminase-Asparaginase

To be Published

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Unit-cell length a length_a	118.260 Å
Unit-cell length b length_b	130.750 Å
Unit-cell length c length_c	85.090 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1650
R_work r_work	0.1650
R_free r_free	—

Description description	GLUTAMINASE-ASPARAGINASE
Molecular weight formula_weight	35978.7 kDa
EC 编号 ec_number	3.5.1.1
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4
Atom count atom_count	10854

STRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE

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

GLUTAMINASE-ASPARAGINASE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (7)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pseudomonas sp. 7A
NCBI Class编号 ncbi_taxonomy_id	65406

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	418

fit	/app/data/saxs_computation/pg/3pga/3pga.fit
pddf	/app/data/pr_computation/pg/3pga/3pga.pr.out
profile	/app/data/saxs_computation/pg/3pga/3pga.dat