SAXSdb — 6rud

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

L-asparaginase

Wolinella succinogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASPG_WOLSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 3–330 Author chain B； PDBConstruct 1–328； UniProt 3–330 Author chain C； PDBConstruct 1–328； UniProt 3–330 Author chain D； PDBConstruct 1–328； UniProt 3–330

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	6rud
Deposition date deposition_date	2019-05-28
Structure title title	WOLINELLA SUCCINOGENES L-ASPARAGINASE P1
Keywords keywords	HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6rud__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6rud__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rud__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.47 Å
Rg (electron density)	29.69 Å
Total Rg	30.60 Å
Atom count	9469
Residues	1275
Excluded volume	169650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rud__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ruda_
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	d6rudb_
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	d6rudc_
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	d6rudd_
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	6rudA01
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	6rudA02
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	6rudB01
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	6rudB02
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	6rudC01
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	6rudC02
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	6rudD01
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	6rudD02
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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Unit-cell length a length_a	62.820 Å
Unit-cell length b length_b	109.170 Å
Unit-cell length c length_c	87.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1621
R_work r_work	0.1604
R_free r_free	0.1939

Description description	L-asparaginase
Molecular weight formula_weight	34701.5 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	A,B,C,D
Atom count atom_count	10438

WOLINELLA SUCCINOGENES L-ASPARAGINASE P1

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

L-asparaginase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rud__assembly_1__model_1

6rud__assembly_1__model_1 | I(q)

6rud__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Wolinella succinogenes
NCBI taxonomy ID ncbi_taxonomy_id	844
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	969

WOLINELLA SUCCINOGENES L-ASPARAGINASE P1

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

L-asparaginase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rud__assembly_1__model_1

6rud__assembly_1__model_1 | I(q)

6rud__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)