SAXSdb — 5i3z

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

L-asparaginase

Dickeya chrysanthemi

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASPG_DICCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–328； UniProt 23–348 Author chain B； PDBConstruct 3–328； UniProt 23–348 Author chain C； PDBConstruct 3–328； UniProt 23–348 Author chain D； PDBConstruct 3–328； UniProt 23–348

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	5i3z
Deposition date deposition_date	2016-02-11
Structure title title	Erwinia chrysanthemi L-asparaginase E63Q mutation + Aspartic acid
Keywords keywords	L-asparaginase, Erwinia chrysanthemum, E63Q mutation, Aspartic acid, 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.

5i3z__assembly_1__model_1

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

Download this curve (.dat)

5i3z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5i3z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.28 Å
Rg (electron density)	29.34 Å
Total Rg	30.27 Å
Atom count	9820
Residues	1300
Excluded volume	175290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5i3z__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 (3)

Entity 1 Entity 1 polymer

Description description	L-asparaginase
Molecular weight formula_weight	35292.3 kDa
EC 编号 ec_number	3.5.1.1
Mutation mutation	E63Q
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10813

HMDKLPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASQNMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	976

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5i3za_
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	d5i3zb_
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	d5i3zc_
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	d5i3zd_
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	5i3zA01
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	5i3zA02
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	5i3zB01
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	5i3zB02
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	5i3zC01
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	5i3zC02
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	5i3zD01
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	5i3zD02
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	77.893 Å
Unit-cell length b length_b	87.885 Å
Unit-cell length c length_c	175.992 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	2.050 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1757
R_work r_work	0.1739
R_free r_free	0.2093

Erwinia chrysanthemi L-asparaginase E63Q mutation + Aspartic acid

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

5i3z__assembly_1__model_1

5i3z__assembly_1__model_1 | I(q)

5i3z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Erwinia chrysanthemi L-asparaginase E63Q mutation + Aspartic acid

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

5i3z__assembly_1__model_1

5i3z__assembly_1__model_1 | I(q)

5i3z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)