SAXSdb — 8z5e

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

3-oxoacyl-[acyl-carrier-protein] synthase 2

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Acyl carrier protein × 1 （Q5EDC8） OCTANOIC ACID (CAPRYLIC ACID) × 2 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Acyl carrier protein × 1 （Q5EDC8） OCTANOIC ACID (CAPRYLIC ACID) × 2 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A438WLJ1_HELPX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–413； UniProt 1–412 Author chain B； PDBConstruct 2–413； UniProt 1–412 Author chain D； PDBConstruct 2–413； UniProt 1–412 Author chain E； PDBConstruct 2–413； UniProt 1–412

Acyl carrier protein

Helicobacter pylori

UniProt Q5EDC8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	3-oxoacyl-[acyl-carrier-protein] synthase 2 × 2 （A0A438WLJ1） OCTANOIC ACID (CAPRYLIC ACID) × 2 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	3-oxoacyl-[acyl-carrier-protein] synthase 2 × 2 （A0A438WLJ1） OCTANOIC ACID (CAPRYLIC ACID) × 2 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5EDC8_HELPX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 9–86； UniProt 1–78 Author chain F； PDBConstruct 9–86； UniProt 1–78

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	8z5e
Deposition date deposition_date	2024-04-18
Structure title title	Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with octanoyl-ACP from Helicobacter pylori
Keywords keywords	beta-ketoacyl-ACP synthase, FabF, octanoyl-ACP, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

8z5e__assembly_1__model_1

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

Download this curve (.dat)

8z5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8z5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.60 Å
Rg (electron density)	26.62 Å
Total Rg	27.42 Å
Atom count	6733
Residues	903
Excluded volume	120150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8z5e__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8z5e__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	3-oxoacyl-[acyl-carrier-protein] synthase 2
Molecular weight formula_weight	43584.7 kDa
EC 编号 ec_number	2.3.1.179
Mutation mutation	K336A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	14286

SMRRIVVTGMGMINSLGLNKEDSFLAIAKGECGIKHIESFDASAFPVRIAGEITDFDPTEVMNPKDVKKAGRFIQLALKATREAMKDSGILDAHNRCPEELANRMGVSSGSGIGGLGNIEANSIFCFEKGPRKVNPFFITSALVNMIGGFTSIEFGIKGPNLSSVTACAAGTHAIIEAVKTILLNGADRMLVVGAESTICPVGIGGFASIKALSTRNDEPKKASRPFDKDRNGFVMGEGAGALVLEEYESAKKRGAKIYAEFAGYGESGDANHITAPAPEGEGAFRAMKMALEMAKVEVGYVNAHGTSTHYNDLYESIALKNVFGSKEKVPPVSSTAGQIGHCLGAAGALEAVISIMAMNQGILPPTINQETPDPECDLDYIPNAAREKQVDAVMSNSFGFGGTNGVVIFKKA

Source Source

Source organism organism	Helicobacter pylori
Common name common_name	Campylobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Acyl carrier protein
Molecular weight formula_weight	9363.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GTSSMGYLMALFEDIQAVIAEQLNVDAAQVTPEAEFVKDLGADSLDVVELIMALEEKFGIEIPDEQAEKIVNVGDVVKYIEDNKLA

Source Source

Source organism organism	Helicobacter pylori
Common name common_name	Campylobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	OCTANOIC ACID (CAPRYLIC ACID)
Molecular weight formula_weight	144.2 kDa
Source method src_method	man
Copy count entity_count	4

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
Molecular weight formula_weight	358.3 kDa
Source method src_method	man
Copy count entity_count	2

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	799

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Unit-cell length a length_a	58.857 Å
Unit-cell length b length_b	115.691 Å
Unit-cell length c length_c	127.933 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	34.520 Å
R factor r_factor	0.1667
R_work r_work	0.1643
R_free r_free	0.2126

Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with octanoyl-ACP from Helicobacter pylori

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

3-oxoacyl-[acyl-carrier-protein] synthase 2

State in the Current Structure

Other States of the Same Protein in the Database

Acyl carrier protein

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

8z5e__assembly_1__model_1

8z5e__assembly_1__model_1 | I(q)

8z5e__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

Source Source

Entity 4 Entity 4 non-polymer

Source Source

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with octanoyl-ACP from Helicobacter pylori

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

3-oxoacyl-[acyl-carrier-protein] synthase 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

Acyl carrier protein

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

8z5e__assembly_1__model_1

8z5e__assembly_1__model_1 | I(q)

8z5e__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

Source Source

Entity 4 Entity 4 non-polymer

Source Source

Entity 5 Entity 5 water

7. Citations (1)