SAXSdb — 1jn9

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

PUTATIVE 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 CHLORIDE ION × 4 CALCIUM ION × 3 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 1–177； UniProt 2–178 Author chain C； PDBConstruct 1–177； UniProt 2–178 Author chain B； PDBConstruct 1–143； UniProt 179–321 Author chain D； PDBConstruct 1–143； UniProt 179–321

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	1jn9
Deposition date deposition_date	2001-07-23
Structure title title	Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene
Keywords keywords	Ntn hydrolase, asparaginase, autoproteolysis, 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.

1jn9__assembly_1__model_1

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

Download this curve (.dat)

1jn9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jn9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.37 Å
Rg (electron density)	23.45 Å
Total Rg	24.30 Å
Atom count	4267
Residues	582
Excluded volume	75951 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jn9__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 (6)

Entity 1 Entity 1 polymer

Description description	PUTATIVE L-ASPARAGINASE
Molecular weight formula_weight	18958.7 kDa
EC 编号 ec_number	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	4526

GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGAPLDEKQKMG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PUTATIVE L-ASPARAGINASE
Molecular weight formula_weight	14428.1 kDa
EC 编号 ec_number	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

TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREKGDTVATQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jn9.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.5 — (Glycosyl)asparaginase

Domain ID domain_id	d1jn9.2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.5 — (Glycosyl)asparaginase

CATH v4.4 (2 domains)

Domain ID domain_id	1jn9B00
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	1jn9D00
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 (7)

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

Acta Crystallogr.,Sect.D (2008)

PMID: 18323626 · DOI: 10.1107/S0907444907068072 PRIMARY

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

Acta Crystallogr.,Sect.D (2000)

DOI: 10.1107/S0907444900010076

Structural insights into the mechanism of intramolecular proteolysis

Cell(Cambridge,Mass.) (1999)

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

Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum

Protein Sci. (1998)

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

J.Biol.Chem. (1998)

DOI: 10.1074/jbc.273.32.20205

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

Nature (1995)

DOI: 10.1038/378416a0

Three-dimensional structure of human lysosomal aspartylglucosaminidase

Nat.Struct.Mol.Biol. (1995)

Unit-cell length a length_a	61.941 Å
Unit-cell length b length_b	70.425 Å
Unit-cell length c length_c	148.862 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	2.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1702
R_work r_work	0.1702
R_free r_free	0.2325

Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene

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

PUTATIVE 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

1jn9__assembly_1__model_1

1jn9__assembly_1__model_1 | I(q)

1jn9__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (7)

Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene

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

PUTATIVE 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

1jn9__assembly_1__model_1

1jn9__assembly_1__model_1 | I(q)

1jn9__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (7)