1dw9

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

Method: X-RAY DIFFRACTION

▼

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

CYANATE LYASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	CHLORIDE ION × 10 SULFATE ION × 23 water × 25	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dw9
Deposition date deposition_date	1999-12-03
Structure title title	Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site
Keywords keywords	LYASE, CYANATE DEGRADATION, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1dw9__assembly_1__model_1

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

Download this curve (.dat)

1dw9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dw9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.25 Å
Rg (electron density)	32.08 Å
Total Rg	32.81 Å
Atom count	12095
Residues	1520
Excluded volume	218860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dw9__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CYANATE LYASE
Molecular weight formula_weight	17255.4 kDa
EC 编号 ec_number	4.3.99.1
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	14178

MIQSQINRNIRLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQMIPLRGCIDDRIPTDPTMYRFYEMLQVYGTTLKALVHEKFGDGIISAINFKLDVKKVADPEGGERAVITLDGKYLPTKPF

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
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	10

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1865

▼

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1dw9a1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9b1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9c1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9d1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9e1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9f1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9f2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9g1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9g2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9h1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9h2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9i1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9i2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

Domain ID domain_id	d1dw9j1
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.4 — Cyanase N-terminal domain

Domain ID domain_id	d1dw9j2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.72 — Cyanase C-terminal domain
Superfamily Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
Family Family family	d.72.1.1 — Cyanase C-terminal domain

CATH v4.4 (20 domains)

Domain ID domain_id	1dw9A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9G02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9I01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9I02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

Domain ID domain_id	1dw9J01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1dw9J02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

▶

Unit-cell length a length_a	76.340 Å
Unit-cell length b length_b	81.030 Å
Unit-cell length c length_c	82.300 Å
Unit-cell angle α angle_alpha	70.30 °
Unit-cell angle β angle_beta	72.20 °
Unit-cell angle γ angle_gamma	66.40 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1500
R_free r_free	0.1890

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

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

CYANATE LYASE

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

1dw9__assembly_1__model_1

1dw9__assembly_1__model_1 | I(q)

1dw9__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) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (5)

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

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

CYANATE LYASE

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

1dw9__assembly_1__model_1

1dw9__assembly_1__model_1 | I(q)

1dw9__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) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (5)