SAXSdb — 3fxd

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

Protein IcmQ

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	Protein IcmR × 1 （Q5ZYC9） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein IcmR × 1 （Q5ZYC9） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5IHF0_LEGPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–57； UniProt 1–57 Author chain C； PDBConstruct 1–57； UniProt 1–57

Protein IcmR

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZYC9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein IcmQ × 1 （A5IHF0） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein IcmQ × 1 （A5IHF0） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC9_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–73； UniProt 23–95 Author chain D； PDBConstruct 1–73； UniProt 23–95

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	3fxd
Deposition date deposition_date	2009-01-20
Structure title title	Crystal structure of interacting domains of IcmR and IcmQ
Keywords keywords	4 helix bundle, helix-turn-helix, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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.

3fxd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fxd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fxd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.26 Å
Rg (electron density)	13.92 Å
Total Rg	15.06 Å
Atom count	822
Residues	107
Excluded volume	14792 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fxd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fxd__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 (3)

Entity 1 Entity 1 polymer

Description description	Protein IcmQ
Molecular weight formula_weight	6510.6 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	1735

MKDQLSDEQKETILKALNDAIEKGPWDKSNFLRVIGKKLIAIRDRFLKRIGAASQAK

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	400673
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein IcmR
Molecular weight formula_weight	7794.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EIGEPDVTDATLGSVYSEIISPVKDCILTVAKAVSFNPGGKDNTDAVEVLTELNTKVERAALNQPILTTKTER

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fxdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	3fxdB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3fxdC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	3fxdD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	90 —

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Unit-cell length a length_a	95.560 Å
Unit-cell length b length_b	95.560 Å
Unit-cell length c length_c	56.010 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
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2500

Crystal structure of interacting domains of IcmR and IcmQ

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

Protein IcmQ

State in the Current Structure

Other States of the Same Protein in the Database

Protein IcmR

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

3fxd__assembly_2__model_1

3fxd__assembly_2__model_1 | I(q)

3fxd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of interacting domains of IcmR and IcmQ

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

Protein IcmQ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein IcmR

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

3fxd__assembly_2__model_1

3fxd__assembly_2__model_1 | I(q)

3fxd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)