SAXSdb — 3l0i

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

DrrA

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-1A × 1 （P62820） SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1A × 1 （P62820） SULFATE ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q29ST3_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–363； UniProt 193–550 Author chain C； PDBConstruct 6–363； UniProt 193–550

Ras-related protein Rab-1A

Homo sapiens

UniProt P62820

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DrrA × 1 （Q29ST3） SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DrrA × 1 （Q29ST3） SULFATE ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 23–199； UniProt 1–177 Author chain D； PDBConstruct 23–199； UniProt 1–177

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	3l0i
Deposition date deposition_date	2009-12-10
Structure title title	Complex structure of SidM/DrrA with the wild type Rab1
Keywords keywords	;GEF-GDF-Rab complex, GTP-binding, guanine-nucleotide exchange factor, GDI-Displacement factor, Type IV effector protein from legionella, PROTEIN BINDING-PROTEIN TRANSPORT complex ;; PROTEIN BINDING/PROTEIN TRANSPORT
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.

3l0i__assembly_1__model_1

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

Download this curve (.dat)

3l0i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3l0i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.11 Å
Rg (electron density)	28.57 Å
Total Rg	29.22 Å
Atom count	3726
Residues	460
Excluded volume	66725 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3l0i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3l0i__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	DrrA
Molecular weight formula_weight	41817.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7704

GPLGSPRYELGEELRDKIKQEPSFSNMVSAKKFYNKAIKDFTAPKEGAEVVSVKTHIMRPIDFMLMGLREEFNLYSEDGAHLSAPGTIRLLREKNLLPEEQIARIESVYNQAMSKRFELHAEHKKEHDEMPYSDAKAMLDEVAKIRELGVQRVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTE

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1A
Molecular weight formula_weight	22894.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MGSSHHHHHHSSGENLYFQGRPMSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMG

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3l0ib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d3l0id_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (6 domains)

Domain ID domain_id	3l0iA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1520 —

Domain ID domain_id	3l0iA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	3l0iB00
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

Domain ID domain_id	3l0iC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1520 —

Domain ID domain_id	3l0iC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	3l0iD00
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	63.808 Å
Unit-cell length b length_b	71.747 Å
Unit-cell length c length_c	146.911 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	34.940 Å
R factor r_factor	0.2300
R_work r_work	0.2260
R_free r_free	0.2660

Complex structure of SidM/DrrA with the wild type Rab1

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

DrrA

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-1A

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

3l0i__assembly_1__model_1

3l0i__assembly_1__model_1 | I(q)

3l0i__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Complex structure of SidM/DrrA with the wild type Rab1

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

DrrA

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-1A

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

3l0i__assembly_1__model_1

3l0i__assembly_1__model_1 | I(q)

3l0i__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)