SAXSdb — 9zsv

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

3-keto-5-aminohexanoate cleavage protein

Burkholderia stagnalis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–299	Not recorded	ZN ZINC ION × 1 COA COENZYME A × 1 A1C39 (2R)-2-acetyl-3-oxo-4-phosphonobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；287 K；28% PEG 4000 100 mM calcium acetate 100 mM sodium acetate (pH=4.5)	Resolution 1.81 Å R-free 0.203
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–299	Not recorded	ZN ZINC ION × 1 COA COENZYME A × 1 A1C39 (2R)-2-acetyl-3-oxo-4-phosphonobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；287 K；28% PEG 4000 100 mM calcium acetate 100 mM sodium acetate (pH=4.5)	Resolution 1.81 Å R-free 0.203

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZSV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZSC Flavophos biosynthetic enzyme BsfD Deposited 2025-12-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–299（299 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；1.6 M lithium sulfate 100 mM Tris HCl, pH=8.5	Resolution 1.72 Å R-free 0.199
9ZSH Flavophos biosynthetic protein BsfD with CoA Deposited 2025-12-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–299（299 aa）	Not recorded	COA COENZYME A × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；1.6 M lithium sulfate 100 mM Tris-HCl, pH=8.5	Resolution 1.50 Å R-free 0.199
9ZSN Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h) Deposited 2025-12-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–299（299 aa）	Not recorded	ZN ZINC ION × 1 COA COENZYME A × 1 A1C39 (2R)-2-acetyl-3-oxo-4-phosphonobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；25% PEG 4000 100 mM calcium acetate 100 mM sodium acetate, pH=4.5	Resolution 1.74 Å R-free 0.204
9ZSN Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h) Deposited 2025-12-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–299（299 aa）	Not recorded	ZN ZINC ION × 1 COA COENZYME A × 1 A1C39 (2R)-2-acetyl-3-oxo-4-phosphonobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；25% PEG 4000 100 mM calcium acetate 100 mM sodium acetate, pH=4.5	Resolution 1.74 Å R-free 0.204

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6L3MU55_9BURK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 1–299 Author chain B； PDBConstruct 1–299； UniProt 1–299

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	9zsv
Deposition date deposition_date	2025-12-22
Structure title title	Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h)
Keywords keywords	Phosphonate BkACE, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.74 Å
Radius of gyration Rg (electron density) rg_electron	25.15 Å
Forward intensity I(0) i0	133236000.00
Molecular weight molecular_weight	59451.0 kDa
Excluded volume excluded_volume	56651 Å³
Envelope volume envelope_volume	93120 Å³
Hydration-shell volume shell_volume	30718 Å³
Envelope diameter envelope_diameter	89.4 Å
Shell Rg shell_rg	32.93 Å
Envelope Rg envelope_rg	25.42 Å
Shape Rg shape_rg	25.18 Å
Total Rg total_rg	25.70 Å
Total atoms total_atoms	4480
Residues n_residues	574
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.5 Å
Rg (real space) rg_real	25.78 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.3320e+08
I(0) uncertainty (real space) i0_real_error	1.8350e+06
Rg (reciprocal space) rg_reciprocal	25.77 Å
I(0) (reciprocal space) i0_reciprocal	133200000.0000
Solution quality estimate total_estimate	0.8082
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.352
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58260000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	3-keto-5-aminohexanoate cleavage protein
Molecular weight formula_weight	32231.1 kDa
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	4908

MATRRTILTCAVTGSQTRLEQNPHLPITPKQIADASLEAADAGAAIVHLHVRDPETGRASMELAHYQEVVDRIRQKNPALIVNITTGPGGRFQPGDVDPAVAGPRTNLLPPERRVAHLPSLRPDIATLDLDTMFFGSEVVINTPPTIRAIARAIHACGAVPELELFDIGNLHLARDLFDEGVLRLPAIASIIVGIKYGMPATTEAMTLARSMLPPGVEWTGFSIGRHAFPMLAQSFVLGGHVRIGMEDTIYIEKGKLAASNAELVDKAKWIVEQLGGELASAEEAREQLRIGEPRALAA

来源 Source

来源生物 organism	Burkholderia stagnalis
NCBI Class编号 ncbi_taxonomy_id	1503054
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	(2R)-2-acetyl-3-oxo-4-phosphonobutanoic acid
Molecular weight formula_weight	224.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	406

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8. Citations (1)

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Unit-cell length a length_a	86.924 Å
Unit-cell length b length_b	109.684 Å
Unit-cell length c length_c	72.521 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	1.810 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1819
R_work r_work	0.1807
R_free r_free	0.2028

fit	/app/data/saxs_computation/zs/9zsv/9zsv.fit
pddf	/app/data/pr_computation/zs/9zsv/9zsv.pr.out
profile	/app/data/saxs_computation/zs/9zsv/9zsv.dat

Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h)

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

3-keto-5-aminohexanoate cleavage protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction