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8dmp

Crystal structure of Legionella pneumophila macrodomain effector MavL

Method: X-RAY DIFFRACTION Dmax: 134.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MavL

Legionella pneumophila

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 42–435 Not recorded No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 42–435 Not recorded No other associated polymer 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 42–435 Not recorded No other associated polymer 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 42–435 Not recorded No other associated polymer 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 42–435 Not recorded No other associated polymer 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
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 42–435 Not recorded No other associated polymer 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
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain G； UniProt 42–435 Not recorded No other associated polymer 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
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain H； UniProt 42–435 Not recorded No other associated polymer 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

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 8DMP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6OMI Crystal structure of the Legionella effector protein MavL Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 42–435（394 aa） Fragment：residues 42-435
Chain B 42–435（394 aa） Fragment：residues 42-435
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
6OMI Crystal structure of the Legionella effector protein MavL Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 42–435（394 aa） 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
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 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 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 mutation/modification 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 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 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 8 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 6–399； UniProt 42–435 Author chain B； PDBConstruct 6–399； UniProt 42–435 Author chain C； PDBConstruct 6–399； UniProt 42–435 Author chain D； PDBConstruct 6–399； UniProt 42–435 Author chain E； PDBConstruct 6–399； UniProt 42–435 Author chain F； PDBConstruct 6–399； UniProt 42–435 Author chain G； PDBConstruct 6–399； UniProt 42–435 Author chain H； PDBConstruct 6–399； 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 8dmp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8dmp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8dmp
Deposition date deposition_date2022-07-08
Structure title titleCrystal structure of Legionella pneumophila macrodomain effector MavL
Keywords keywordsMacrodomain, Effector, Glycohydrolase, ANTITOXIN; ANTITOXIN
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_guinier45.67 Å
Radius of gyration Rg (electron density) rg_electron44.75 Å
Forward intensity I(0) i01516300000.00
Molecular weight molecular_weight323100.0 kDa
Excluded volume excluded_volume403560 ų
Envelope volume envelope_volume539330 ų
Hydration-shell volume shell_volume96019 ų
Envelope diameter envelope_diameter137.7 Å
Shell Rg shell_rg53.71 Å
Envelope Rg envelope_rg43.01 Å
Shape Rg shape_rg44.74 Å
Total Rg total_rg45.12 Å
Total atoms total_atoms22812
Residues n_residues2963
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 dmax134.1 Å
Rg (real space) rg_real45.25 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real1.5160e+09
I(0) uncertainty (real space) i0_real_error2.2030e+07
Rg (reciprocal space) rg_reciprocal45.67 Å
I(0) (reciprocal space) i0_reciprocal1517000000.0000
Solution quality estimate total_estimate0.8834
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.3 Å
Skewness Skewness skewness-0.056
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha174300000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.810
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)