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5czy

Crystal structure of LegAS4

Method: X-RAY DIFFRACTION Dmax: 80.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Legionella effector LegAS4

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZUS4

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 63–545 Fragment：UNP residues 63-545 GOL GLYCEROL × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M sodium citrate, 15 % (v/v) isopropanol, 10%(w/v) PEG 10000 Resolution 2.20 Å R-free 0.248

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 5CZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SR6 Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide Deposited 2023-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 84–532（449 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 10 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
Resolution 2.22 Å R-free 0.230
8SWI Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (1-12)peptide Deposited 2023-05-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 84–532（449 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
Resolution 3.00 Å R-free 0.310

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5ZUS4_LEGPH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–483； UniProt 63–545

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 5czy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5czy
Deposition date deposition_date2015-08-01
Structure title titleCrystal structure of LegAS4
Keywords keywordsSET domain, TRANSFERASE; TRANSFERASE
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_guinier25.67 Å
Radius of gyration Rg (electron density) rg_electron24.72 Å
Forward intensity I(0) i045706800.00
Molecular weight molecular_weight52316.0 kDa
Excluded volume excluded_volume65443 ų
Envelope volume envelope_volume80707 ų
Hydration-shell volume shell_volume27276 ų
Envelope diameter envelope_diameter85.8 Å
Shell Rg shell_rg31.78 Å
Envelope Rg envelope_rg24.86 Å
Shape Rg shape_rg24.70 Å
Total Rg total_rg25.63 Å
Total atoms total_atoms3688
Residues n_residues449
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 dmax80.8 Å
Rg (real space) rg_real25.60 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real4.5710e+07
I(0) uncertainty (real space) i0_real_error6.3950e+05
Rg (reciprocal space) rg_reciprocal25.62 Å
I(0) (reciprocal space) i0_reciprocal45710000.0000
Solution quality estimate total_estimate0.9094
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.7 Å
Skewness Skewness skewness0.210
Kurtosis Kurtosis kurtosis-0.574
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8970000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992
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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)