SAXSdb — 6exe

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

IcmP (DotM)

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 5 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC7_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–235； UniProt 153–380 Author chain B； PDBConstruct 8–235； UniProt 153–380

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	6exe
Deposition date deposition_date	2017-11-08
Structure title title	Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E
Keywords keywords	Membrane protein, secretion system, type 4 secretion system, Legionella pneumophila, coupling complex, PROTEIN BINDING; PROTEIN BINDING
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.

6exe__assembly_1__model_1

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

Download this curve (.dat)

6exe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6exe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.13 Å
Rg (electron density)	27.00 Å
Total Rg	27.84 Å
Atom count	3581
Residues	442
Excluded volume	64148 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6exe__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 (4)

Entity 1 Entity 1 polymer

Description description	IcmP (DotM)
Molecular weight formula_weight	26480.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3721

GPSGGGADVNKGPWAMALTPMEFARKYNLLRKDDALLDNPVPGEEMTAGIRRGDAKRVFTMQLGPYWDGFEECSPQAYALSAVFMARMNRDRDAANNILKVLDKTFVDGKPDFSVARPVMKKYQNSELVQEVVAKHAYVLTVIASLLEAAREDGVVPSSEFLWLKPVDRRLWYMLNCVGRQTPYSEVAGPFAHWKAEKEMGRRSLVPMIDEAIRALEIAVKEVRLTPRQMEELEP

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	134

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Unit-cell length a length_a	118.278 Å
Unit-cell length b length_b	118.278 Å
Unit-cell length c length_c	66.571 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	53.450 Å
R factor r_factor	0.2251
R_work r_work	0.2230
R_free r_free	0.2644

Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E

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

IcmP (DotM)

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

6exe__assembly_1__model_1

6exe__assembly_1__model_1 | I(q)

6exe__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E

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

IcmP (DotM)

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

6exe__assembly_1__model_1

6exe__assembly_1__model_1 | I(q)

6exe__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)