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5ufk

Structure of the effector protein SidK (lpg0968) from Legionella pneumophila

Method: X-RAY DIFFRACTION Dmax: 92.1 Å Quality: REASONABLE
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 16–278 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

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 5UFK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UF5 Structure of the effector protein SidK (lpg0968) from Legionella pneumophila (domain-swapped dimer) Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–278（263 aa）
Chain B 16–278（263 aa）
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
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

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 5ufk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5ufk
Deposition date deposition_date2017-01-04
Structure title titleStructure of the effector protein SidK (lpg0968) from Legionella pneumophila
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_guinier25.23 Å
Radius of gyration Rg (electron density) rg_electron24.93 Å
Forward intensity I(0) i014711200.00
Molecular weight molecular_weight29602.0 kDa
Excluded volume excluded_volume37354 ų
Envelope volume envelope_volume46107 ų
Hydration-shell volume shell_volume17666 ų
Envelope diameter envelope_diameter93.8 Å
Shell Rg shell_rg28.49 Å
Envelope Rg envelope_rg25.48 Å
Shape Rg shape_rg24.93 Å
Total Rg total_rg25.38 Å
Total atoms total_atoms2081
Residues n_residues256
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 dmax92.1 Å
Rg (real space) rg_real25.62 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real1.4710e+07
I(0) uncertainty (real space) i0_real_error2.1320e+05
Rg (reciprocal space) rg_reciprocal25.50 Å
I(0) (reciprocal space) i0_reciprocal14710000.0000
Solution quality estimate total_estimate0.7440
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.9 Å
Skewness Skewness skewness0.696
Kurtosis Kurtosis kurtosis-0.038
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3365000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.509; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.251; Smooth: 0.890
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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)