SAXSdb — 3c17

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

L-asparaginase precursor

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 11 CHLORIDE ION × 17 water × 2	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
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 2–321 Author chain B； PDBConstruct 1–320； UniProt 2–321

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	3c17
Deposition date deposition_date	2008-01-22
Structure title title	Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation
Keywords keywords	ISOASPARTYL PEPTIDASE, ASPARAGINASE, NTN-HYDROLASE, AUTOPROTEOLYSIS, PRECURSOR, 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.

3c17__assembly_1__model_1

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

Download this curve (.dat)

3c17__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c17__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.61 Å
Rg (electron density)	23.67 Å
Total Rg	24.49 Å
Atom count	4470
Residues	611
Excluded volume	79739 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c17__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	L-asparaginase precursor
Molecular weight formula_weight	33262.7 kDa
EC 编号 ec_number	3.4.19.5, 3.5.1.1
Mutation mutation	T179A
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	4968

GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGAPLDEKQKMGAVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREKGDTVATQ

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	434

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7. Citations (11)

The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases

J.Biol.Chem. (2008)

PMID: 18334484 · DOI: 10.1074/jbc.M800746200 PRIMARY

Crystal structure of plant asparaginase

J.Mol.Biol. (2006)

PMID: 16725155 · DOI: 10.1016/j.jmb.2006.04.066

Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate

J.Biol.Chem. (2005)

PMID: 15946951 · DOI: 10.1074/jbc.M504501200

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

Acta Crystallogr.,Sect.D (2004)

PMID: 15159592 · DOI: 10.1107/S0907444904003403

A dual role for an aspartic acid in glycosylasparaginase autoproteolysis

Structure (2003)

PMID: 12906830 · DOI: 10.1016/S0969-2126(03)00150-3

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

Characterization and functional analysis of the cis-autoproteolysis active center of glycosylasparaginase

J.Biol.Chem. (1998)

PMID: 9545304 · DOI: 10.1074/jbc.273.16.9695

Activation and oligomerization of aspartylglucosaminidase

J.Biol.Chem. (1998)

PMID: 9737998 · DOI: 10.1074/jbc.273.39.25320

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

Nature (1995)

PMID: 7477383 · DOI: 10.1038/378416a0

Crystal packing of plant-type L-asparaginase from Escherichia coli

To be Published

Unit-cell length a length_a	149.470 Å
Unit-cell length b length_b	149.470 Å
Unit-cell length c length_c	214.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	44.510 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2030

Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation

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

L-asparaginase precursor

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

3c17__assembly_1__model_1

3c17__assembly_1__model_1 | I(q)

3c17__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (11)

Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation

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

L-asparaginase precursor

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

3c17__assembly_1__model_1

3c17__assembly_1__model_1 | I(q)

3c17__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (11)