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6omi

Crystal structure of the Legionella effector protein MavL

Method: X-RAY DIFFRACTION Dmax: 114.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MavL

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

UniProt Q5ZSJ1

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 42–435 Chain B； UniProt 42–435 Fragment：residues 42-435 Non-standard monomer：Yes (specific site not provided by mmCIF) BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；20% PEG8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5 Resolution 2.64 Å R-free 0.253
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 42–435 Fragment：residues 42-435 Non-standard monomer：Yes (specific site not provided by mmCIF) BR BROMIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；20% PEG8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5 Resolution 2.64 Å R-free 0.253

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 6OMI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 42–435（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, 18% w/v PEG 3350
Resolution 2.17 Å R-free 0.214
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different mutation/modification 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 42–435（394 aa）
Not recorded FLC CITRATE ANION × 4 EDO 1,2-ETHANEDIOL × 2 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 42–435（394 aa）
Not recorded FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMR Legionella macrodomain effector MavL R370A in complex with ADP-ribose Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–435（394 aa）
Mutation：R370A AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M ammonium sulfate
Resolution 1.86 Å R-free 0.180
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different mutation/modification 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 42–435（394 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 42–435（394 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 GVE METHYL 4-AMINOBUTANOATE × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8XEP Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin Deposited 2023-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–455（455 aa）
Chain D 1–455（455 aa）
Mutation：C226A Mutation：C226A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM sodium acetate, pH 6.0, 160 mM ammonium sulfate, 21% PEG 4000, 20% glycerol
Resolution 2.95 Å R-free 0.228

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5ZSJ1_LEGPH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–396； UniProt 42–435 Author chain B； PDBConstruct 3–396； UniProt 42–435 Author chain C； PDBConstruct 3–396； UniProt 42–435

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 6omi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6omi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6omi
Deposition date deposition_date2019-04-18
Structure title titleCrystal structure of the Legionella effector protein MavL
Keywords keywordsADP-ribosyltransferase (ART), macrodomain, Secreted bacterial effector protein, HYDROLASE; HYDROLASE
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_guinier34.58 Å
Radius of gyration Rg (electron density) rg_electron34.28 Å
Forward intensity I(0) i0218742000.00
Molecular weight molecular_weight115730.0 kDa
Excluded volume excluded_volume142610 ų
Envelope volume envelope_volume180530 ų
Hydration-shell volume shell_volume44101 ų
Envelope diameter envelope_diameter117.4 Å
Shell Rg shell_rg40.51 Å
Envelope Rg envelope_rg34.24 Å
Shape Rg shape_rg34.32 Å
Total Rg total_rg34.57 Å
Total atoms total_atoms8094
Residues n_residues1060
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 dmax114.2 Å
Rg (real space) rg_real34.63 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real2.1870e+08
I(0) uncertainty (real space) i0_real_error3.8510e+06
Rg (reciprocal space) rg_reciprocal34.61 Å
I(0) (reciprocal space) i0_reciprocal218700000.0000
Solution quality estimate total_estimate0.6609
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.8 Å
Skewness Skewness skewness0.359
Kurtosis Kurtosis kurtosis-0.473
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48140000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.986; Smooth: 0.842
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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)