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9zsc

Flavophos biosynthetic enzyme BsfD

Method: X-RAY DIFFRACTION Dmax: 61.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-keto-5-aminohexanoate cleavage protein

Burkholderia stagnalis

UniProt A0A6L3MU55

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 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

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 9ZSC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 ligand/ion 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
9ZSV Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h) 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 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
9ZSV Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h) Deposited 2025-12-22 Different ligand/ion 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；28% PEG 4000 100 mM calcium acetate 100 mM sodium acetate (pH=4.5)
Resolution 1.81 Å R-free 0.203

3 other PDB entries and 5 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9zsc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zsc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zsc
Deposition date deposition_date2025-12-22
Structure title titleFlavophos biosynthetic enzyme BsfD
Keywords keywordsPhosphonate BkACE, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.04 Å
Radius of gyration Rg (electron density) rg_electron17.94 Å
Forward intensity I(0) i018133200.00
Molecular weight molecular_weight31967.0 kDa
Excluded volume excluded_volume39952 ų
Envelope volume envelope_volume45614 ų
Hydration-shell volume shell_volume20642 ų
Envelope diameter envelope_diameter63.9 Å
Shell Rg shell_rg24.98 Å
Envelope Rg envelope_rg18.23 Å
Shape Rg shape_rg17.95 Å
Total Rg total_rg18.88 Å
Total atoms total_atoms2242
Residues n_residues295
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.9 Å
Rg (real space) rg_real18.89 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.8130e+07
I(0) uncertainty (real space) i0_real_error2.3830e+05
Rg (reciprocal space) rg_reciprocal18.91 Å
I(0) (reciprocal space) i0_reciprocal18130000.0000
Solution quality estimate total_estimate0.6180
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.4200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6812000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.771; Stabil: 0.999; Sysdev: 0.242; Positv: 1.000; Valcen: 0.992; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)