SAXSdb — 1vpm

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

acyl-CoA hydrolase

Bacillus halodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	COENZYME A × 4 PHOSPHATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KEQ1_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–169； UniProt 1–157 Author chain B； PDBConstruct 13–169； UniProt 1–157 Author chain C； PDBConstruct 13–169； UniProt 1–157

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	1vpm
Deposition date deposition_date	2004-11-11
Structure title title	Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution
Keywords keywords	;NP_241664.1, ACYL-COA HYDROLASE, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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.

1vpm__assembly_1__model_1

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

Download this curve (.dat)

1vpm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vpm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.63 Å
Rg (electron density)	28.38 Å
Total Rg	29.06 Å
Atom count	7164
Residues	900
Excluded volume	126810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vpm__assembly_1__model_1`	hexameric （6）	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	acyl-CoA hydrolase
Molecular weight formula_weight	19047.8 kDa
EC 编号 ec_number	3.1.2.-
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	3951

MGSDKIHHHHHHMIQSYPVERSRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHANSAVVTASIDSVDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHSNNLLTGERTLTTESFLTMVAVDESGKPKPVPQVEPQTEEEKRLYETAPARKENRKKRAALR

Source Source

Source organism organism	Bacillus halodurans
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	310

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vpma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.1 — 4HBT-like

Domain ID domain_id	d1vpmb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.1 — 4HBT-like

Domain ID domain_id	d1vpmc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.1 — 4HBT-like

Domain ID domain_id	d1vpmc2
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 (3 domains)

Domain ID domain_id	1vpmA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	1vpmB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	1vpmC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

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Unit-cell length a length_a	82.984 Å
Unit-cell length b length_b	106.507 Å
Unit-cell length c length_c	120.254 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	24

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	1.660 Å
Low-resolution limit resolution_low	28.750 Å
R factor r_factor	0.1715
R_work r_work	0.1701
R_free r_free	0.1967

Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution

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

acyl-CoA hydrolase

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

1vpm__assembly_1__model_1

1vpm__assembly_1__model_1 | I(q)

1vpm__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 (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

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution

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

acyl-CoA hydrolase

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

1vpm__assembly_1__model_1

1vpm__assembly_1__model_1 | I(q)

1vpm__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 (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

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)