1d0i

CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS

Method: X-RAY DIFFRACTION

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

TYPE II 3-DEHYDROQUINATE HYDRATASE

Streptomyces coelicolor

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	PHOSPHATE ION × 16 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AROQ_STRCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 2–157 Author chain B； PDBConstruct 1–156； UniProt 2–157 Author chain C； PDBConstruct 1–156； UniProt 2–157 Author chain D； PDBConstruct 1–156； UniProt 2–157 Author chain E； PDBConstruct 1–156； UniProt 2–157 Author chain F； PDBConstruct 1–156； UniProt 2–157 Author chain G； PDBConstruct 1–156； UniProt 2–157 Author chain H； PDBConstruct 1–156； UniProt 2–157 Author chain I； PDBConstruct 1–156； UniProt 2–157 Author chain J； PDBConstruct 1–156； UniProt 2–157 Author chain K； PDBConstruct 1–156； UniProt 2–157 Author chain L； PDBConstruct 1–156； UniProt 2–157

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	1d0i
Deposition date deposition_date	1999-09-10
Structure title title	CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS
Keywords keywords	TYPE II DEHYDROQUINASE, SHIKIMATE PATHWAY, DODECAMERIC QUATERNARY STRUCTURE, TETRAHEDRAL SYMMETRY, 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.

1d0i__assembly_1__model_1

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

Download this curve (.dat)

1d0i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d0i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.94 Å
Rg (electron density)	35.12 Å
Total Rg	35.81 Å
Atom count	13681
Residues	1810
Excluded volume	239240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d0i__assembly_1__model_1`	dodecameric （12）	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	TYPE II 3-DEHYDROQUINATE HYDRATASE
Molecular weight formula_weight	16569.6 kDa
EC 编号 ec_number	4.2.1.10
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	15962

PRSLANAPIMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHEARLNHCGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAGCGVQGYVFGVERIAALAGAGSARA

Source Source

Source organism organism	Streptomyces coelicolor
NCBI taxonomy ID ncbi_taxonomy_id	1902
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2023

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1d0ia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0id_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ie_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0if_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ig_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ih_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ii_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ij_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0ik_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1d0il_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

CATH v4.4 (12 domains)

Domain ID domain_id	1d0iA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1d0iL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

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Unit-cell length a length_a	113.200 Å
Unit-cell length b length_b	137.500 Å
Unit-cell length c length_c	140.200 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	45.030 Å
R factor r_factor	0.1760
R_work r_work	0.1710
R_free r_free	0.2230

CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS

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

TYPE II 3-DEHYDROQUINATE HYDRATASE

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

1d0i__assembly_1__model_1

1d0i__assembly_1__model_1 | I(q)

1d0i__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS

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

TYPE II 3-DEHYDROQUINATE HYDRATASE

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

1d0i__assembly_1__model_1

1d0i__assembly_1__model_1 | I(q)

1d0i__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)