3r7d

Crystal Structure of Unliganded Aspartate Transcarbamoylase from Bacillus subtilis

Method: X-RAY DIFFRACTION

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

Aspartate carbamoyltransferase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRB_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–304； UniProt 1–304 Author chain B； PDBConstruct 1–304； UniProt 1–304 Author chain C； PDBConstruct 1–304； UniProt 1–304

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	3r7d
Deposition date deposition_date	2011-03-22
Structure title title	Crystal Structure of Unliganded Aspartate Transcarbamoylase from Bacillus subtilis
Keywords keywords	Aspartate Transcarbamoylase, Transferase, Catalytic Cycle; TRANSFERASE
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.

3r7d__assembly_1__model_1

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

Download this curve (.dat)

3r7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.62 Å
Rg (electron density)	30.64 Å
Total Rg	31.21 Å
Atom count	6927
Residues	873
Excluded volume	122380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r7d__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Aspartate carbamoyltransferase
Molecular weight formula_weight	34266.7 kDa
EC 编号 ec_number	2.1.3.2
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	7587

MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQTNVKRGEAAYVISH

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	583

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3r7da1
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.78.1.0 — automated matches

Domain ID domain_id	d3r7da2
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.78.1.0 — automated matches

Domain ID domain_id	d3r7db1
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.78.1.0 — automated matches

Domain ID domain_id	d3r7db2
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.78.1.0 — automated matches

Domain ID domain_id	d3r7dc1
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.78.1.0 — automated matches

Domain ID domain_id	d3r7dc2
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.78.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3r7dA01
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	3r7dA02
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	3r7dB01
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	3r7dB02
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	3r7dC01
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	3r7dC02
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

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Unit-cell length a length_a	253.470 Å
Unit-cell length b length_b	153.016 Å
Unit-cell length c length_c	51.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.196 Å
Low-resolution limit resolution_low	49.173 Å
R factor r_factor	0.1690
R_work r_work	0.1677
R_free r_free	0.1950

Crystal Structure of Unliganded Aspartate Transcarbamoylase from Bacillus subtilis

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

Aspartate carbamoyltransferase

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

3r7d__assembly_1__model_1

3r7d__assembly_1__model_1 | I(q)

3r7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Unliganded Aspartate Transcarbamoylase from Bacillus subtilis

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

Aspartate carbamoyltransferase

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

3r7d__assembly_1__model_1

3r7d__assembly_1__model_1 | I(q)

3r7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)