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3roh

Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.

Method: X-RAY DIFFRACTION Dmax: 85.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Leucotoxin LukEv

Staphylococcus aureus subsp. aureus NCTC 8325

UniProt Q2FXB0

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 1–306 Not recorded PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；Protein: 7mG/mL, 0.25M Sodium chloride, 0.01M Tris, pH 8.3. Screen: JCSG+, D7, 0.2M Lithium sulfate, 0.1M Tris, pH 8.5, 40% v/v PEG 400. VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 3.20 Å R-free 0.224

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 3ROH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7P8S Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.9 Angstrom resolution Deposited 2021-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded P6G HEXAETHYLENE GLYCOL × 1 MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Ammonium sulfate, 0.05 M Magnesium sulfate heptahydrate, 0.1 M Sodium citrate pH 5.5 and 22.5 % v/v PEG Smear Medium
Resolution 1.90 Å R-free 0.203
7P8T Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.5 Angstrom resolution Deposited 2021-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.46 Å R-free 0.194
7P8U Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with p-cresyl sulfate Deposited 2021-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 IMD IMIDAZOLE × 1 SO4 SULFATE ION × 1 6EI (4-methylphenyl) hydrogen sulfate × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.60 Å R-free 0.205
7P8X Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a doubly sulfated CCR2 N-terminal peptide Deposited 2021-07-23 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 7–306（300 aa）
Not recorded IMD IMIDAZOLE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.40 Å R-free 0.198
7P93 Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide Deposited 2021-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 7–306（300 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.55 Å R-free 0.204

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUKEV_STAA8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–329； UniProt 1–306

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 3roh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3roh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3roh
Deposition date deposition_date2011-04-25
Structure title titleCrystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.
Keywords keywords;Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, Leukocidin-like, Leukocidin, pore-forming toxin, Membrane and cell surface proteins and peptides, TOXIN ;; TOXIN
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_guinier23.06 Å
Radius of gyration Rg (electron density) rg_electron22.40 Å
Forward intensity I(0) i017986500.00
Molecular weight molecular_weight31980.0 kDa
Excluded volume excluded_volume39952 ų
Envelope volume envelope_volume47779 ų
Hydration-shell volume shell_volume19114 ų
Envelope diameter envelope_diameter88.3 Å
Shell Rg shell_rg27.79 Å
Envelope Rg envelope_rg23.11 Å
Shape Rg shape_rg22.36 Å
Total Rg total_rg23.25 Å
Total atoms total_atoms2260
Residues n_residues282
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 dmax85.2 Å
Rg (real space) rg_real23.30 Å
Rg uncertainty (real space) rg_real_error0.99 Å
I(0) (real space) i0_real1.7990e+07
I(0) uncertainty (real space) i0_real_error2.9140e+05
Rg (reciprocal space) rg_reciprocal23.24 Å
I(0) (reciprocal space) i0_reciprocal17990000.0000
Solution quality estimate total_estimate0.7845
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.3 Å
Skewness Skewness skewness0.631
Kurtosis Kurtosis kurtosis-0.064
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5806000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.534; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.613; Smooth: 0.981
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3rohA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology240 — Leukocidin-like
Homologous superfamily homologous superfamily10 — Leukocidin/porin MspA
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8. Citations (1)

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9. Files and Curves (10)