SAXSdb — 8dmr

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1. Protein Identity and Related Structures Protein Identity & Related Structures

MavL

Legionella pneumophila

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	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

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 8DMR	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
8DMP Crystal structure of Legionella pneumophila macrodomain effector MavL 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）	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08	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 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 15 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8dmr
Deposition date deposition_date	2022-07-08
Structure title title	Legionella macrodomain effector MavL R370A in complex with ADP-ribose
Keywords keywords	Complex, Macrodomain, Metaeffector, ANTITOXIN; ANTITOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.89 Å
Radius of gyration Rg (electron density) rg_electron	19.71 Å
Forward intensity I(0) i0	29763200.00
Molecular weight molecular_weight	41392.0 kDa
Excluded volume excluded_volume	51521 Å³
Envelope volume envelope_volume	58315 Å³
Hydration-shell volume shell_volume	23813 Å³
Envelope diameter envelope_diameter	64.2 Å
Shell Rg shell_rg	27.07 Å
Envelope Rg envelope_rg	20.10 Å
Shape Rg shape_rg	19.70 Å
Total Rg total_rg	20.67 Å
Total atoms total_atoms	5587
Residues n_residues	373
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.2 Å
Rg (real space) rg_real	20.74 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	2.9760e+07
I(0) uncertainty (real space) i0_real_error	3.4550e+05
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	29760000.0000
Solution quality estimate total_estimate	0.9026
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.107
Kurtosis Kurtosis kurtosis	-0.483
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6964000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	MavL
Molecular weight formula_weight	44094.5 kDa
Mutation mutation	R370A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5896

GPLGSAYQLLLSKETLNKILQYKQNLEKGLATPGKFFLEELSKQEKSISEMDITTFTQLLIQSKKPQVFAESQVYHDGTDWTLEEESILGDVSVNMPVTMYNDGGHGSSFKNHPKPISGYLAYVPGALLASGSGPTSDMKEVLDNGKLNQDKLNALYERRLLPQLIHFNELARQNEKQAAITIPGIGTGCFSGAYYDVIKPYVRNALIHILEKHKDSLPYIDIIHYDPYMGDEPAEKKIGHMSFRVSPSGVVRGTTGQLDYPLGSNPDTHILVSIVAWDHFSWPGNDYWGGARQTDDGVKAASTDTMGQVTGATGVYDKKWGRYMPPESFTKDAKGMSDWGDYVRENGIVFNGPVLALDKSGKLDTLENVASRSSKAKVETTTTISDLVRSMFSLFSHS

来源 Source

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	446
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;[(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 ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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8. Citations (1)

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Unit-cell length a length_a	95.557 Å
Unit-cell length b length_b	95.557 Å
Unit-cell length c length_c	54.046 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	tetragonal

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	42.210 Å
R factor r_factor	0.1520
R_work r_work	0.1506
R_free r_free	0.1798

fit	/app/data/saxs_computation/dm/8dmr/8dmr.fit
pddf	/app/data/pr_computation/dm/8dmr/8dmr.pr.out
profile	/app/data/saxs_computation/dm/8dmr/8dmr.dat

Legionella macrodomain effector MavL R370A in complex with ADP-ribose

1. Protein Identity and Related Structures Protein Identity & Related Structures

MavL

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction