SAXSdb — 8agg

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

Phosphocholine hydrolase Lem3

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 1–570	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；MES 0.1M pH 5, PEG6000 5%	Resolution 3.60 Å R-free 0.299

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 8AGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ALK Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1 Deposited 2022-08-01	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 21–486（466 aa）	Mutation：T391C, C395S, C134S, C209S, C456S	CA CALCIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 OJU 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；MES 0.1M pH 5, PEG6000 5%	Resolution 2.15 Å R-free 0.228
8ANP Legionella effector Lem3 mutant D190A in complex with Mg2+ Deposited 2022-08-05	Different construct 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 21–486（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES; 30% PEG 300	Resolution 2.20 Å R-free 0.230
8ANP Legionella effector Lem3 mutant D190A in complex with Mg2+ Deposited 2022-08-05	Different construct 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 21–486（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES; 30% PEG 300	Resolution 2.20 Å R-free 0.230
8ANP Legionella effector Lem3 mutant D190A in complex with Mg2+ Deposited 2022-08-05	Different construct 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 21–486（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES; 30% PEG 300	Resolution 2.20 Å R-free 0.230
8ANP Legionella effector Lem3 mutant D190A in complex with Mg2+ Deposited 2022-08-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 21–486（466 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.1 M MES; 30% PEG 300	Resolution 2.20 Å R-free 0.230

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

View Construct and Data Evidence

UniProt name	LEM3_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–572； UniProt 1–570

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	8agg
Deposition date deposition_date	2022-07-20
Structure title title	Structure of the Legionella phosphocholine hydrolase Lem3
Keywords keywords	Bacterial effector, dephosphocholinase, Legionella pneumophila, HYDROLASE; HYDROLASE
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	28.94 Å
Radius of gyration Rg (electron density) rg_electron	29.18 Å
Forward intensity I(0) i0	49518900.00
Molecular weight molecular_weight	54598.0 kDa
Excluded volume excluded_volume	68234 Å³
Envelope volume envelope_volume	88883 Å³
Hydration-shell volume shell_volume	27995 Å³
Envelope diameter envelope_diameter	121.0 Å
Shell Rg shell_rg	32.79 Å
Envelope Rg envelope_rg	30.28 Å
Shape Rg shape_rg	29.19 Å
Total Rg total_rg	29.52 Å
Total atoms total_atoms	3843
Residues n_residues	489
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	114.8 Å
Rg (real space) rg_real	29.34 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	4.9520e+07
I(0) uncertainty (real space) i0_real_error	8.3480e+05
Rg (reciprocal space) rg_reciprocal	29.17 Å
I(0) (reciprocal space) i0_reciprocal	49510000.0000
Solution quality estimate total_estimate	0.7093
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.792
Kurtosis Kurtosis kurtosis	0.385
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13220000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.354; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.258; Smooth: 0.899

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Phosphocholine hydrolase Lem3
Molecular weight formula_weight	65020.7 kDa
EC 编号 ec_number	3.1.3.-
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	3843

GHMKLRYIINENKLVFTSCNMRDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEHDTILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNCDQNIDTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGDGLIIILDKRFKIKHMVSACHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVWGELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKTLIKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIEIPLEMVMHDLKSRTVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEADLEEAFHRLSLEMVQPEIECPISETHFERAFKKETLDKTQAVLTHYFRISTGLDSKKNYQERLNDLSAYLSKESSLEKNDIKLLLSMLDSEIKPKTGVFQTLFGENQNKLYKAFHKKIELQLLDSEIENKNELK

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	78.022 Å
Unit-cell length b length_b	78.022 Å
Unit-cell length c length_c	382.014 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	66.540 Å
R factor r_factor	0.2643
R_work r_work	0.2626
R_free r_free	0.2988

fit	/app/data/saxs_computation/ag/8agg/8agg.fit
pddf	/app/data/pr_computation/ag/8agg/8agg.pr.out
profile	/app/data/saxs_computation/ag/8agg/8agg.dat

Structure of the Legionella phosphocholine hydrolase Lem3

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

Phosphocholine hydrolase Lem3

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)