2zal

Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate

Method: X-RAY DIFFRACTION

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

L-asparaginase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 2 CALCIUM ION × 5 ASPARTIC ACID × 5 CHLORIDE ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASGX_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 2–161 Author chain C； PDBConstruct 1–160； UniProt 2–161 Author chain B； PDBConstruct 1–137； UniProt 179–315 Author chain D； PDBConstruct 1–137； UniProt 179–315

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	2zal
Deposition date deposition_date	2007-10-07
Structure title title	Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate
Keywords keywords	isoaspartyl peptidase, asparaginase, Ntn-hydrolase, autoproteolysis, L-aspartate/calcium cluster, 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.

2zal__assembly_1__model_1

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

Download this curve (.dat)

2zal__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zal__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.27 Å
Rg (electron density)	23.35 Å
Total Rg	24.18 Å
Atom count	4328
Residues	586
Excluded volume	76915 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zal__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 (8)

Entity 1 Entity 1 polymer

Description description	L-asparaginase
Molecular weight formula_weight	17071.5 kDa
EC 编号 ec_number	3.4.19.5, 3.5.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4598

GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	L-asparaginase
Molecular weight formula_weight	13812.5 kDa
EC 编号 ec_number	3.4.19.5, 3.5.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREKG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2zalB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	30 — (Glycosyl)asparaginase

Domain ID domain_id	2zalD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	30 — (Glycosyl)asparaginase

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7. Citations (9)

Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate

J.Biol.Chem. (2005)

PMID: 15946951 · DOI: 10.1074/jbc.M504501200 PRIMARY

Autoproteolytic activation of human aspartylglucosaminidase

Biochem.J. (2004)

PMID: 14616088 · DOI: 10.1042/BJ20031496

Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli

Acta Crystallogr.,Sect.D (2004)

PMID: 15159592 · DOI: 10.1107/S0907444904003403

Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome

Acta Crystallogr.,Sect.D (2000)

PMID: 11053866 · DOI: 10.1107/S0907444900010076

Structural insights into the mechanism of intramolecular proteolysis

Cell(Cambridge,Mass.) (1999)

PMID: 10490104 · DOI: 10.1016/S0092-8674(00)80052-5

Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum

Protein Sci. (1998)

PMID: 9541410

;Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis ;

J.Biol.Chem. (1998)

PMID: 9685368 · DOI: 10.1074/jbc.273.32.20205

A protein catalytic framework with an N-terminal nucleophile is capable of self-activation

Nature (1995)

PMID: 7477383 · DOI: 10.1038/378416a0

Three-dimensional structure of human lysosomal aspartylglucosaminidase

Nat.Struct.Biol. (1995)

PMID: 8846222 · DOI: 10.1038/nsb1295-1102

Unit-cell length a length_a	49.890 Å
Unit-cell length b length_b	77.280 Å
Unit-cell length c length_c	147.530 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	8

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	20.000 Å
R factor r_factor	0.1580
R_work r_work	0.1570
R_free r_free	0.1880

Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate

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

2zal__assembly_1__model_1

2zal__assembly_1__model_1 | I(q)

2zal__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (9)

Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate

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

2zal__assembly_1__model_1

2zal__assembly_1__model_1 | I(q)

2zal__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (9)