6paa

E. coli L-asparaginase II mutant (T12V) in complex with L-Asp at pH 5.5

Method: X-RAY DIFFRACTION

▼

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

L-asparaginase 2

Escherichia coli (strain K12)

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
2	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	ASPG2_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–334； UniProt 23–348 Author chain B； PDBConstruct 9–334； UniProt 23–348 Author chain C； PDBConstruct 9–334； UniProt 23–348 Author chain D； PDBConstruct 9–334； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6paa
Deposition date deposition_date	2019-06-11
Structure title title	E. coli L-asparaginase II mutant (T12V) in complex with L-Asp at pH 5.5
Keywords keywords	inactive mutant, hydrolysis of L-asparagine, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6paa__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6paa__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6paa__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.46 Å
Rg (electron density)	29.53 Å
Total Rg	30.39 Å
Atom count	9426
Residues	1252
Excluded volume	167450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6paa__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6paa__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	L-asparaginase 2
Molecular weight formula_weight	35700.0 kDa
EC 编号 ec_number	3.5.1.1
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	10469

MDHHHHHHLPNITILATGGVIAGGGDSATKSNYTVGKVGVENLVNAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

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	1075

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6paaa1
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	d6paaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6paab1
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	d6paab2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6paac1
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	d6paac2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6paad1
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	d6paad2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	6paaA01
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	6paaA02
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	6paaB01
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	6paaB02
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	6paaC01
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	6paaC02
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	6paaD01
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	6paaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	40 —

▶

Unit-cell length a length_a	151.837 Å
Unit-cell length b length_b	62.472 Å
Unit-cell length c length_c	143.373 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1727
R_work r_work	0.1699
R_free r_free	0.2286

E. coli L-asparaginase II mutant (T12V) in complex with L-Asp at pH 5.5

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

L-asparaginase 2

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

6paa__assembly_2__model_1

6paa__assembly_2__model_1 | I(q)

6paa__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

E. coli L-asparaginase II mutant (T12V) in complex with L-Asp at pH 5.5

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

L-asparaginase 2

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

6paa__assembly_2__model_1

6paa__assembly_2__model_1 | I(q)

6paa__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)