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9wyx

Cryo-EM structure of PbSS

Method: ELECTRON MICROSCOPY Dmax: 124.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sesterbrasiliatriene synthase PbSS

Penicillium brasilianum

UniProt A0A2Z6AQX7

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–732 Chain B； UniProt 1–732 Chain C； UniProt 1–732 Chain D； UniProt 1–732 Chain E； UniProt 1–732 Chain F； UniProt 1–732 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.04 Å

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 9WYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8YL9 Crystal structures of terpene synthases complexed with a substrate mimic Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–352（352 aa）
Chain B 1–352（352 aa）
Chain I 1–352（352 aa）
Not recorded MG MAGNESIUM ION × 9 PPV PYROPHOSPHATE × 3 BTM N-benzyl-N,N-diethylethanaminium × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM Magnesium formate and 26% w/v PEG3350
Resolution 2.75 Å R-free 0.268
8YL9 Crystal structures of terpene synthases complexed with a substrate mimic Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–352（352 aa）
Not recorded MG MAGNESIUM ION × 3 PPV PYROPHOSPHATE × 1 BTM N-benzyl-N,N-diethylethanaminium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM Magnesium formate and 26% w/v PEG3350
Resolution 2.75 Å R-free 0.268
8YL9 Crystal structures of terpene synthases complexed with a substrate mimic Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–352（352 aa）
Not recorded MG MAGNESIUM ION × 3 PPV PYROPHOSPHATE × 1 BTM N-benzyl-N,N-diethylethanaminium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM Magnesium formate and 26% w/v PEG3350
Resolution 2.75 Å R-free 0.268
8YL9 Crystal structures of terpene synthases complexed with a substrate mimic Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 1–352（352 aa）
Not recorded MG MAGNESIUM ION × 3 PPV PYROPHOSPHATE × 1 BTM N-benzyl-N,N-diethylethanaminium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM Magnesium formate and 26% w/v PEG3350
Resolution 2.75 Å R-free 0.268

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

View Construct and Data Evidence
UniProt name PBSS_PENBI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–732； UniProt 1–732 Author chain B； PDBConstruct 1–732； UniProt 1–732 Author chain C； PDBConstruct 1–732； UniProt 1–732 Author chain D； PDBConstruct 1–732； UniProt 1–732 Author chain E； PDBConstruct 1–732； UniProt 1–732 Author chain F； PDBConstruct 1–732； UniProt 1–732

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 9wyx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9wyx
Deposition date deposition_date2025-09-28
Structure title titleCryo-EM structure of PbSS
Keywords keywordsSesterbrasiliatriene synthase PbSS, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.04 Å
Radius of gyration Rg (electron density) rg_electron40.69 Å
Forward intensity I(0) i0576904000.00
Molecular weight molecular_weight195230.0 kDa
Excluded volume excluded_volume243930 ų
Envelope volume envelope_volume328830 ų
Hydration-shell volume shell_volume66868 ų
Envelope diameter envelope_diameter132.2 Å
Shell Rg shell_rg46.67 Å
Envelope Rg envelope_rg39.66 Å
Shape Rg shape_rg40.63 Å
Total Rg total_rg41.23 Å
Total atoms total_atoms13692
Residues n_residues1710
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 dmax124.3 Å
Rg (real space) rg_real40.87 Å
Rg uncertainty (real space) rg_real_error0.99 Å
I(0) (real space) i0_real5.7690e+08
I(0) uncertainty (real space) i0_real_error9.5100e+06
Rg (reciprocal space) rg_reciprocal41.04 Å
I(0) (reciprocal space) i0_reciprocal577000000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.4 Å
Skewness Skewness skewness0.109
Kurtosis Kurtosis kurtosis-0.578
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57900000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.839
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)