5x0z

Crystal structure of FliM-SpeE complex from H. pylori

Method: X-RAY DIFFRACTION

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

Polyamine aminopropyltransferase

Helicobacter pylori 26695

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Flagellar motor switch protein (FliM) × 1 （O25675） CITRATE ANION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Flagellar motor switch protein (FliM) × 1 （O25675） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPEE_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–264； UniProt 1–262 Author chain B； PDBConstruct 3–264； UniProt 1–262 Author chain C； PDBConstruct 3–264； UniProt 1–262 Author chain D； PDBConstruct 3–264； UniProt 1–262

Flagellar motor switch protein (FliM)

Helicobacter pylori 26695

UniProt O25675

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Polyamine aminopropyltransferase × 2 （O25503） CITRATE ANION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Polyamine aminopropyltransferase × 2 （O25503） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O25675_HELPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–197； UniProt 43–237 Author chain F； PDBConstruct 3–197； UniProt 43–237

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	5x0z
Deposition date deposition_date	2017-01-23
Structure title title	Crystal structure of FliM-SpeE complex from H. pylori
Keywords keywords	flagellar motor, H. pylori, motility, TRANSFERASE-MOTOR PROTEIN complex; TRANSFERASE/MOTOR PROTEIN
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.

5x0z__assembly_1__model_1

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

Download this curve (.dat)

5x0z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5x0z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.08 Å
Rg (electron density)	28.99 Å
Total Rg	29.86 Å
Atom count	5773
Residues	709
Excluded volume	104290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5x0z__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5x0z__assembly_2__model_1`	trimeric （3）	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	Polyamine aminopropyltransferase
Molecular weight formula_weight	30729.7 kDa
EC 编号 ec_number	2.5.1.22, 2.5.1.16
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11598

GSMWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Flagellar motor switch protein (FliM)
Molecular weight formula_weight	22074.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GSKRPNRVSKEQLRSFRSIHDKMARNLSSQVSSIMRSIVEIQLHSVDQMTYGEFLMSLPSPTSFNVFSMKPMGGTGVLEINPSIAFPMIDRLLGGKGSAYDQNREFSDIELNLLDTILRQVMQILKEVWSPVVEMFPTIDAKESSANVVQIVAQNEISIMVVLEIIIGHSRGMMNICYPVISIESILSKMGSRDLML

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 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	87

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5x0za_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d5x0zb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d5x0zc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d5x0zd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	5x0zA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	5x0zA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5x0zB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	5x0zB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5x0zC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	5x0zC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5x0zD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	140 — Spermidine Synthase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Spermidine synthase, tetramerisation domain

Domain ID domain_id	5x0zD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5x0zE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1550 — Chemotaxis protein chec
Homologous superfamily homologous superfamily	10 — CheC-like

Domain ID domain_id	5x0zF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1550 — Chemotaxis protein chec
Homologous superfamily homologous superfamily	10 — CheC-like

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Unit-cell length a length_a	184.314 Å
Unit-cell length b length_b	184.314 Å
Unit-cell length c length_c	157.083 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	24

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	27.050 Å
R factor r_factor	0.1790
R_work r_work	0.1770
R_free r_free	0.2160

Crystal structure of FliM-SpeE complex from H. pylori

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

Polyamine aminopropyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Flagellar motor switch protein (FliM)

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

5x0z__assembly_1__model_1

5x0z__assembly_1__model_1 | I(q)

5x0z__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of FliM-SpeE complex from H. pylori

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

Polyamine aminopropyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Flagellar motor switch protein (FliM)

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

5x0z__assembly_1__model_1

5x0z__assembly_1__model_1 | I(q)

5x0z__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)