SAXSdb — 8alk

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） CALCIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1 ;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 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEM3_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–469； UniProt 21–486

Ras-related protein Rab-1B

Homo sapiens

UniProt Q9H0U4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phosphocholine hydrolase Lem3 × 1 （Q5ZXN5） CALCIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1 ;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 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB1B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–175； UniProt 3–174

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	8alk
Deposition date deposition_date	2022-08-01
Structure title title	Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1
Keywords keywords	Bacterial effector, dephosphocholinase, Legionella pneumophila, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8alk__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8alk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8alk__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.12 Å
Rg (electron density)	28.79 Å
Total Rg	29.20 Å
Atom count	4856
Residues	610
Excluded volume	86435 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8alk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Phosphocholine hydrolase Lem3
Molecular weight formula_weight	52900.6 kDa
EC 编号 ec_number	3.1.3.-
Mutation mutation	T391C, C395S, C134S, C209S, C456S
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	4940

GHMDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEHDTILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNSDQNIDTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGDGLIIILDKRFKIKHMVSASHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVWGELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKTLIKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIEIPLEMVMHDLKSRCVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEADLEEAFHRLSLEMVQPEIESPISETHFERAFKKETLDKTQAVLTHYFRIS

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1B
Molecular weight formula_weight	19725.4 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	S76T
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSTYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;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 ;
Molecular weight formula_weight	608.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8alkB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	119.332 Å
Unit-cell length b length_b	119.332 Å
Unit-cell length c length_c	79.058 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	103.340 Å
R factor r_factor	0.1837
R_work r_work	0.1813
R_free r_free	0.2275

Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1

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

Ras-related protein Rab-1B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8alk__assembly_1__model_1

8alk__assembly_1__model_1 | I(q)

8alk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related protein Rab-1B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8alk__assembly_1__model_1

8alk__assembly_1__model_1 | I(q)

8alk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)