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5uf5

Structure of the effector protein SidK (lpg0968) from Legionella pneumophila (domain-swapped dimer)

Method: X-RAY DIFFRACTION Dmax: 118.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

effector protein SidK

Legionella pneumophila

UniProt G8UUS6

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 16–278 Chain B； UniProt 16–278 Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate trihydrate pH 6.5, 0.2 M magnesium acetate tetrahydrate, 20% (w/v) polyethylene glycol 8,000 Resolution 2.40 Å R-free 0.230

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 5UF5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UFK Structure of the effector protein SidK (lpg0968) from Legionella pneumophila Deposited 2017-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–278（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M TRIS hydrochloride pH 8.5, 0.2 M lithium sulfate monohydrate and 30% (w/v) polyethylene glycol 4,000
Resolution 2.30 Å R-free 0.212
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain e 1–573（573 aa）
Chain f 1–573（573 aa）
Chain g 1–573（573 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain e 1–573（573 aa）
Chain f 1–573（573 aa）
Chain g 1–573（573 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain e 1–573（573 aa）
Chain f 1–573（573 aa）
Chain g 1–573（573 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å

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

View Construct and Data Evidence
UniProt name G8UUS6_LEGPN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–266； UniProt 16–278 Author chain B； PDBConstruct 4–266； UniProt 16–278

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 5uf5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5uf5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5uf5
Deposition date deposition_date2017-01-03
Structure title titleStructure of the effector protein SidK (lpg0968) from Legionella pneumophila (domain-swapped dimer)
Keywords keywordstranslocated effector, V-ATPase binding, all-alpha-helical, PROTEIN BINDING; PROTEIN BINDING
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_guinier30.57 Å
Radius of gyration Rg (electron density) rg_electron30.09 Å
Forward intensity I(0) i050844300.00
Molecular weight molecular_weight56038.0 kDa
Excluded volume excluded_volume70083 ų
Envelope volume envelope_volume90465 ų
Hydration-shell volume shell_volume26723 ų
Envelope diameter envelope_diameter122.5 Å
Shell Rg shell_rg34.52 Å
Envelope Rg envelope_rg30.70 Å
Shape Rg shape_rg30.14 Å
Total Rg total_rg30.32 Å
Total atoms total_atoms3945
Residues n_residues516
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 dmax118.5 Å
Rg (real space) rg_real30.94 Å
Rg uncertainty (real space) rg_real_error1.33 Å
I(0) (real space) i0_real5.0840e+07
I(0) uncertainty (real space) i0_real_error8.9200e+05
Rg (reciprocal space) rg_reciprocal30.78 Å
I(0) (reciprocal space) i0_reciprocal50840000.0000
Solution quality estimate total_estimate0.7753
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.2 Å
Skewness Skewness skewness0.679
Kurtosis Kurtosis kurtosis0.302
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11380000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.548; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.486; Smooth: 0.945
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)