2glv

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori

Method: X-RAY DIFFRACTION

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5G940_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–171； UniProt 1–159 Author chain B； PDBConstruct 13–171； UniProt 1–159 Author chain C； PDBConstruct 13–171； UniProt 1–159 Author chain D； PDBConstruct 13–171； UniProt 1–159 Author chain E； PDBConstruct 13–171； UniProt 1–159 Author chain F； PDBConstruct 13–171； UniProt 1–159 Author chain G； PDBConstruct 13–171； UniProt 1–159 Author chain H； PDBConstruct 13–171； UniProt 1–159 Author chain I； PDBConstruct 13–171； UniProt 1–159 Author chain J； PDBConstruct 13–171； UniProt 1–159 Author chain K； PDBConstruct 13–171； UniProt 1–159 Author chain L； PDBConstruct 13–171； UniProt 1–159

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	2glv
Deposition date deposition_date	2006-04-05
Structure title title	Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori
Keywords keywords	FabZ mutant, Lyase; LYASE
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.

2glv__assembly_1__model_1

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

Download this curve (.dat)

2glv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2glv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.54 Å
Rg (electron density)	27.33 Å
Total Rg	28.44 Å
Atom count	7277
Residues	908
Excluded volume	131870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2glv__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2glv__assembly_2__model_1`	hexameric （6）	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	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
Molecular weight formula_weight	19519.6 kDa
EC 编号 ec_number	4.2.1.-
Mutation mutation	Y100A
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	14745

MRGSHHHHHHGSMEQSHQNLQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVAFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	102617
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2glva_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glve_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

Domain ID domain_id	d2glvl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.6 — FabZ-like

CATH v4.4 (12 domains)

Domain ID domain_id	2glvA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvH00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvJ00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2glvL00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

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Unit-cell length a length_a	266.525 Å
Unit-cell length b length_b	76.913 Å
Unit-cell length c length_c	113.187 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2400
R_free r_free	0.2930

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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

2glv__assembly_1__model_1

2glv__assembly_1__model_1 | I(q)

2glv__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori

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

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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

2glv__assembly_1__model_1

2glv__assembly_1__model_1 | I(q)

2glv__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)