2be7

Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda

Method: X-RAY DIFFRACTION

▼

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

Aspartate Carbamoyltransferase Catalytic Chain

Moritella profunda

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Aspartate Carbamoyltransferase Regulatory Chain × 6 （P96175） SULFATE ION × 6 ZINC ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRB_VIBS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–324； UniProt 1–307 Author chain B； PDBConstruct 18–324； UniProt 1–307 Author chain C； PDBConstruct 18–324； UniProt 1–307

Aspartate Carbamoyltransferase Regulatory Chain

Moritella profunda

UniProt P96175

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Aspartate Carbamoyltransferase Catalytic Chain × 6 （P96174） SULFATE ION × 6 ZINC ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRI_VIBS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–153； UniProt 1–153 Author chain E； PDBConstruct 1–153； UniProt 1–153 Author chain F； PDBConstruct 1–153； UniProt 1–153

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	2be7
Deposition date deposition_date	2005-10-23
Structure title title	Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda
Keywords keywords	ATCASE, PSYCHROPHILIC, COLD ADAPTATION, TRANSFERASE, ALLOSTERIC, HOLOENZYME; TRANSFERASE
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.

2be7__assembly_1__model_1

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

Download this curve (.dat)

2be7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2be7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.75 Å
Rg (electron density)	42.15 Å
Total Rg	42.48 Å
Atom count	19846
Residues	2630
Excluded volume	352780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2be7__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Aspartate Carbamoyltransferase Catalytic Chain
Molecular weight formula_weight	36266.8 kDa
EC 编号 ec_number	2.1.3.2
Mutation mutation	V2A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9959

MGSSHHHHHHSQDPNSMANPLFRKHIVSINDISRNELELIVKTAAKLKEQPQPELLKNKVIASCFFEASTRTRLSFETAIQRLGGSVIGFDNAGNTSLAKKGETLADSISVISSYADAFVMRHPQEGAARLASEFSNVPVINGGDGSNQHPTQTLLDLFSIYETQGRLDNLNIAFVGDLKYGRTVHSLAQALAKFDGCKFHFIAPDALAMPEYICDELDEQNISYATYASIEEVVPEIDVLYMTRVQKERFDETEYQHMKAGFILSASSLVHAKPNLKVLHPLPRVDEIATDVDKTPYAYYFQQAENGVYAREALLALVLNETIGE

Source Source

Source organism organism	Moritella profunda
NCBI taxonomy ID ncbi_taxonomy_id	111291
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Aspartate Carbamoyltransferase Regulatory Chain
Molecular weight formula_weight	16911.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MKNNHMQVEAICNGYVIDHIPSGQGVKILKLFSLTDTKQRVTVGFNLPTKDGNAKDLIKVENTEITKSQANQLALLAPNATINIIENFKVTDKHSLTLPNEVENVFPCPNSNCITHGEPVTSSFSIKKTKGNIGLKCKYCEKTFSKDIVTEQV

Source Source

Source organism organism	Moritella profunda
NCBI taxonomy ID ncbi_taxonomy_id	111291
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2be7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d2be7d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
Family Family family	d.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain

Domain ID domain_id	d2be7d2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
Family Family family	g.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

Domain ID domain_id	d2be7e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
Family Family family	d.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain

Domain ID domain_id	d2be7e2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
Family Family family	g.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

Domain ID domain_id	d2be7f1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
Family Family family	d.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain

Domain ID domain_id	d2be7f2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
Family Family family	g.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	2be7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	2be7D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain

Domain ID domain_id	2be7D02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

Domain ID domain_id	2be7E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain

Domain ID domain_id	2be7E02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

Domain ID domain_id	2be7F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain

Domain ID domain_id	2be7F02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

▶

Unit-cell length a length_a	129.238 Å
Unit-cell length b length_b	129.238 Å
Unit-cell length c length_c	207.232 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2139
R_work r_work	0.2116
R_free r_free	0.2570

Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda

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

Aspartate Carbamoyltransferase Catalytic Chain

State in the Current Structure

Other States of the Same Protein in the Database

Aspartate Carbamoyltransferase Regulatory Chain

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

2be7__assembly_1__model_1

2be7__assembly_1__model_1 | I(q)

2be7__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (2)

Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda

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

Aspartate Carbamoyltransferase Catalytic Chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Aspartate Carbamoyltransferase Regulatory Chain

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

2be7__assembly_1__model_1

2be7__assembly_1__model_1 | I(q)

2be7__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (2)