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9wfd

Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus

Method: ELECTRON MICROSCOPY Dmax: 179.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Type II and III secretion system protein

Acidithiobacillus caldus (strain SM-1)

UniProt F9ZTP9

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 × 14 PDB declaration: 14-meric（14） Consistent with protein copy count Chain A； UniProt 1–502 Chain B； UniProt 1–502 Chain C； UniProt 1–502 Chain D； UniProt 1–502 Chain E； UniProt 1–502 Chain F； UniProt 1–502 Chain G； UniProt 1–502 Chain H； UniProt 1–502 Chain I； UniProt 1–502 Chain J； UniProt 1–502 Chain K； UniProt 1–502 Chain L； UniProt 1–502 Chain M； UniProt 1–502 Chain N； UniProt 1–502 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.39 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 9WFD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8JVB Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus Deposited 2023-06-28 Parsed fields agree Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–502（502 aa）
Chain B 1–502（502 aa）
Chain C 1–502（502 aa）
Chain D 1–502（502 aa）
Chain E 1–502（502 aa）
Chain F 1–502（502 aa）
Chain G 1–502（502 aa）
Chain H 1–502（502 aa）
Chain I 1–502（502 aa）
Chain J 1–502（502 aa）
Chain K 1–502（502 aa）
Chain L 1–502（502 aa）
Chain M 1–502（502 aa）
Chain N 1–502（502 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å

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

View Construct and Data Evidence
UniProt name F9ZTP9_ACICS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–502； UniProt 1–502 Author chain B； PDBConstruct 1–502； UniProt 1–502 Author chain C； PDBConstruct 1–502； UniProt 1–502 Author chain D； PDBConstruct 1–502； UniProt 1–502 Author chain E； PDBConstruct 1–502； UniProt 1–502 Author chain F； PDBConstruct 1–502； UniProt 1–502 Author chain G； PDBConstruct 1–502； UniProt 1–502 Author chain H； PDBConstruct 1–502； UniProt 1–502 Author chain I； PDBConstruct 1–502； UniProt 1–502 Author chain J； PDBConstruct 1–502； UniProt 1–502 Author chain K； PDBConstruct 1–502； UniProt 1–502 Author chain L； PDBConstruct 1–502； UniProt 1–502 Author chain M； PDBConstruct 1–502； UniProt 1–502 Author chain N； PDBConstruct 1–502； UniProt 1–502

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 9wfd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9wfd
Deposition date deposition_date2025-08-21
最后修订 last_revision2025-11-19
Structure title titleCryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
Keywords keywords--Type II secretion system protein, Acidithiobacillus caldus, TOXIN; TOXIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier66.59 Å
Radius of gyration Rg (electron density) rg_electron66.17 Å
Forward intensity I(0) i05579570000.00
Molecular weight molecular_weight643520.0 kDa
Excluded volume excluded_volume811780 ų
Envelope volume envelope_volume1510900 ų
Hydration-shell volume shell_volume185510 ų
Envelope diameter envelope_diameter189.6 Å
Shell Rg shell_rg75.61 Å
Envelope Rg envelope_rg61.75 Å
Shape Rg shape_rg66.18 Å
Total Rg total_rg66.30 Å
Total atoms total_atoms45332
Residues n_residues6034
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 dmax179.6 Å
Rg (real space) rg_real65.89 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real5.5800e+09
I(0) uncertainty (real space) i0_real_error9.9810e+07
Rg (reciprocal space) rg_reciprocal67.17 Å
I(0) (reciprocal space) i0_reciprocal5592000000.0000
Solution quality estimate total_estimate0.8310
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary97.3 Å
Skewness Skewness skewness-0.044
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha614600000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.013
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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)