SAXSdb — 9w96

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

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

Agrobacterium fabrum str. C58

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	glutaryl-coenzyme A × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	glutaryl-coenzyme A × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIOZ_AGRFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–327； UniProt 2–328 Author chain B； PDBConstruct 1–327； UniProt 2–328 Author chain C； PDBConstruct 1–327； UniProt 2–328 Author chain D； PDBConstruct 1–327； UniProt 2–328

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	9w96
Deposition date deposition_date	2025-08-09
Structure title title	Crystal structure of BioZ C115S from Agrobacterium tumefaciens in complex with galutaryl-CoA
Keywords keywords	BioZ, 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.

9w96__assembly_1__model_1

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

Download this curve (.dat)

9w96__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9w96__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.14 Å
Rg (electron density)	23.78 Å
Total Rg	24.63 Å
Atom count	4869
Residues	653
Excluded volume	85961 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9w96__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9w96__assembly_2__model_1`	dimeric （2）	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	3-oxopimeloyl-[acyl-carrier-protein] synthase
Molecular weight formula_weight	34022.6 kDa
EC 编号 ec_number	2.3.1.-
Mutation mutation	C115S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9931

QTRSSRMAGFGHAVPARCVDNAEIEASLGLEAGWIERRTGIRSRYWAEAGDTLSGLAERAGRMALEDAKINADDIALTLLATSTPDHLLPPSAPLLAHRLGLTRSGAIDLAGASSGFLYALTLADGFVRTYGRAVLVVAANILSRRINPAERASAVLFADAAGAVVLTPCPEVKRGVLSADLVADGSGYDLIQIAAGGSSQPFSAGMIAEDALMTMRDGREVFSRAVALMTNTSQRVLHEAELTAADISRFVPHQANARMSDAVCGNLGIEREKTVRTIGSFGNSSAATIPLSLSITNAERPLAGGETLLLTAAGAGMTGGAVVYRV

Source Source

Source organism organism	Agrobacterium fabrum str. C58
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	glutaryl-coenzyme A
Molecular weight formula_weight	881.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

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Unit-cell length a length_a	62.718 Å
Unit-cell length b length_b	128.453 Å
Unit-cell length c length_c	170.961 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.050 Å
R factor r_factor	0.2179
R_work r_work	0.2160
R_free r_free	0.2538

Crystal structure of BioZ C115S from Agrobacterium tumefaciens in complex with galutaryl-CoA

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

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

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

9w96__assembly_1__model_1

9w96__assembly_1__model_1 | I(q)

9w96__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of BioZ C115S from Agrobacterium tumefaciens in complex with galutaryl-CoA

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

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

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

9w96__assembly_1__model_1

9w96__assembly_1__model_1 | I(q)

9w96__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)