SAXSdb — 2hfk

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

Type I polyketide synthase PikAIV

Streptomyces venezuelae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 MAGNESIUM ION × 1 DIMETHYL SULFOXIDE × 4 (3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-4-HYDROXY-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 6 MAGNESIUM ION × 2 DIMETHYL SULFOXIDE × 8 (3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-4-HYDROXY-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZGI2_9ACTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–319； UniProt 1049–1346 Author chain B； PDBConstruct 22–319； UniProt 1049–1346

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	2hfk
Deposition date deposition_date	2006-06-24
Structure title title	Pikromycin thioesterase in complex with product 10-deoxymethynolide
Keywords keywords	alpha/beta hydrolase, thioesterase, 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.

2hfk__assembly_1__model_1

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

Download this curve (.dat)

2hfk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hfk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.20 Å
Rg (electron density)	29.75 Å
Total Rg	30.14 Å
Atom count	4275
Residues	557
Excluded volume	75381 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hfk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hfk__assembly_2__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	Type I polyketide synthase PikAIV
Molecular weight formula_weight	33771.8 kDa
Mutation mutation	S148A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4989

MGSSHHHHHHSSGLVPRGSHMSGADTGAGAGMFRALFRQAVEDDRYGEFLDVLAEASAFRPQFASPEACSERLDPVLLAGGPTDRAEGRAVLVGCTGTAANGGPHEFLRLSTSFQEERDFLAVPLPGYGTGTGTGTALLPADLDTALDAQARAILRAAGDAPVVLLGHAGGALLAHELAFRLERAHGAPPAGIVLVDPYPPGHQEPIEVWSRQLGEGLFAGELEPMSDARLLAMGRYARFLAGPRPGRSSAPVLLVRASEPLGDWQEERGDWRAHWDLPHTVADVPGDHFTMMRDHAPAVAEAVLSWLDAIEGIEGAGK

Source Source

Source organism organism	Streptomyces venezuelae
NCBI taxonomy ID ncbi_taxonomy_id	54571
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	(3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-4-HYDROXY-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE
Molecular weight formula_weight	296.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	648

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2hfka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.22 — Thioesterase domain of polypeptide, polyketide and fatty acid synthases

Domain ID domain_id	d2hfkb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.22 — Thioesterase domain of polypeptide, polyketide and fatty acid synthases

CATH v4.4 (2 domains)

Domain ID domain_id	2hfkA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	2hfkB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	108.051 Å
Unit-cell length b length_b	131.076 Å
Unit-cell length c length_c	57.512 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.790 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1941
R_work r_work	0.1922
R_free r_free	0.2297

Pikromycin thioesterase in complex with product 10-deoxymethynolide

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

Type I polyketide synthase PikAIV

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

2hfk__assembly_1__model_1

2hfk__assembly_1__model_1 | I(q)

2hfk__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 non-polymer

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 (1)

Pikromycin thioesterase in complex with product 10-deoxymethynolide

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

Type I polyketide synthase PikAIV

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

2hfk__assembly_1__model_1

2hfk__assembly_1__model_1 | I(q)

2hfk__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 non-polymer

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 (1)