2ae8

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

Method: X-RAY DIFFRACTION

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

Imidazoleglycerol-phosphate dehydratase

Staphylococcus aureus subsp. aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 24	MAGNESIUM ION × 64 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIS7_STAAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–221； UniProt 1–192 Author chain B； PDBConstruct 30–221； UniProt 1–192 Author chain C； PDBConstruct 30–221； UniProt 1–192 Author chain D； PDBConstruct 30–221； UniProt 1–192 Author chain E； PDBConstruct 30–221； UniProt 1–192 Author chain F； PDBConstruct 30–221； UniProt 1–192

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	2ae8
Deposition date deposition_date	2005-07-21
Structure title title	Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315
Keywords keywords	;beta-alpha-beta sandwich, duplication of a half-domain, imidazoleglycerol-phosphate dehydratase (IGPD), Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2ae8__assembly_1__model_1

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

Download this curve (.dat)

2ae8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ae8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.62 Å
Rg (electron density)	48.40 Å
Total Rg	48.93 Å
Atom count	32484
Residues	3984
Excluded volume	581680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ae8__assembly_1__model_1`	24-meric （24）	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	Imidazoleglycerol-phosphate dehydratase
Molecular weight formula_weight	24845.1 kDa
EC 编号 ec_number	4.2.1.19
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9237

HHHHHHSSGVDLGTENLYFQSNIGSGSNAMIYQKQRNTAETQLNISISDDQSPSHINTGVGFLNHMLTLFTFHSGLSLNIEAQGDIDVDDHHVTEDIGIVIGQLLLEMIKDKKHFVRYGTMYIPMDETLARVVVDISGRPYLSFNASLSKEKVGTFDTELVEEFFRAVVINARLTTHIDLIRGGNTHHEIEAIFKAFSRALGIALTATDDQRVPSSKGVIE

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	946

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d2ae8a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ae8c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8e3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ae8f1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

Domain ID domain_id	d2ae8f2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.9 — Imidazole glycerol phosphate dehydratase

CATH v4.4 (12 domains)

Domain ID domain_id	2ae8A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

Domain ID domain_id	2ae8F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	40 — Imidazole glycerol phosphate dehydratase; domain 1

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Unit-cell length a length_a	129.247 Å
Unit-cell length b length_b	129.247 Å
Unit-cell length c length_c	180.143 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	40.800 Å
R factor r_factor	0.1916
R_work r_work	0.1877
R_free r_free	0.2263

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

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

Imidazoleglycerol-phosphate 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

2ae8__assembly_1__model_1

2ae8__assembly_1__model_1 | I(q)

2ae8__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) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

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

Imidazoleglycerol-phosphate 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

2ae8__assembly_1__model_1

2ae8__assembly_1__model_1 | I(q)

2ae8__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) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)