SAXSdb — 1rhy

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

Imidazole glycerol phosphate dehydratase

Filobasidiella neoformans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MERCURY (II) ION × 3 ETHYL MERCURY ION × 6 SULFATE ION × 9 GLYCEROL × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	MERCURY (II) ION × 3 ETHYL MERCURY ION × 6 SULFATE ION × 6 GLYCEROL × 18 ACETIC ACID × 21 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIS7_CRYNE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 1–202 Author chain B； PDBConstruct 1–202； UniProt 1–202

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	1rhy
Deposition date deposition_date	2003-11-14
Structure title title	Crystal structure of Imidazole Glycerol Phosphate Dehydratase
Keywords keywords	dehydratases; histidine biosynthesis; left-handed b-a-b crossover motif; gene duplication, 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.

1rhy__assembly_1__model_1

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

Download this curve (.dat)

1rhy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rhy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.35 Å
Rg (electron density)	24.96 Å
Total Rg	26.11 Å
Atom count	4221
Residues	540
Excluded volume	75217 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rhy__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rhy__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 (7)

Entity 1 Entity 1 polymer

Description description	Imidazole glycerol phosphate dehydratase
Molecular weight formula_weight	22008.1 kDa
EC 编号 ec_number	4.2.1.19
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	3141

MSERIASVERTTSETHISCTIDLDHIPGVTEQKINVSTGIGFLDHMFTALAKHGGMSLQLQCKGDLHIDDHHTAEDCALALGEAFKKALGERKGIKRYGYAYAPLDESLSRAVIDISSRPYFMCHLPFTREKVGDLSTEMVSHLLQSFAFAAGVTLHIDSIRGENNHHIAESAFKALALAIRMAISRTGGDDVPSTKGVLAL

Source Source

Source organism organism	Filobasidiella neoformans
NCBI taxonomy ID ncbi_taxonomy_id	5207
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ETHYL MERCURY ION
Molecular weight formula_weight	229.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rhya1
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	d1rhya2
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	d1rhyb1
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	d1rhyb2
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 (4 domains)

Domain ID domain_id	1rhyA01
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	1rhyA02
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	1rhyB01
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	1rhyB02
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	105.275 Å
Unit-cell length b length_b	105.275 Å
Unit-cell length c length_c	105.275 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.550 Å
R factor r_factor	0.1891
R_work r_work	0.1890
R_free r_free	0.2280

Crystal structure of Imidazole Glycerol Phosphate Dehydratase

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

Imidazole glycerol 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

1rhy__assembly_1__model_1

1rhy__assembly_1__model_1 | I(q)

1rhy__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Imidazole Glycerol Phosphate Dehydratase

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

Imidazole glycerol 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

1rhy__assembly_1__model_1

1rhy__assembly_1__model_1 | I(q)

1rhy__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)