2ivg

SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE

Method: X-RAY DIFFRACTION

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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	SULFATE ION × 29 CHLORIDE ION × 20 AZIDE ION × 1 water × 10	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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ivg
Deposition date deposition_date	2006-06-13
Structure title title	SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE
Keywords keywords	MIDWEST CENTER FOR STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, MCSG, LYASE, CYANATE DEGRADATION; 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.

2ivg__assembly_1__model_1

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

Download this curve (.dat)

2ivg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ivg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.17 Å
Rg (electron density)	32.00 Å
Total Rg	32.81 Å
Atom count	12079
Residues	1560
Excluded volume	217610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ivg__assembly_1__model_1`	decameric （10）	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 (5)

Entity 1 Entity 1 polymer

Description description	CYANATE LYASE
Molecular weight formula_weight	17011.7 kDa
EC 编号 ec_number	4.2.1.104
Mutation mutation	YES
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	13926

MIQSQINRNIRLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQMIPLRGCIDDRIPTDPTMYRFYEMLQVYGTTLKALVHEKFGDGIISAINFKLDVKKVADPEGGERAVITLDGKYGPTKPF

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	29

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 4 Entity 4 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1754

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d2ivga1
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	d2ivga2
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	d2ivgb1
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	d2ivgb2
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	d2ivgc1
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	d2ivgc2
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	d2ivgd1
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	d2ivgd2
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	d2ivge1
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	d2ivge2
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	d2ivgf1
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	d2ivgf2
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	d2ivgg1
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	d2ivgg2
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	d2ivgh1
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	d2ivgh2
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	d2ivgi1
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	d2ivgi2
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	d2ivgj1
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	d2ivgj2
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	2ivgA01
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	2ivgA02
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	2ivgB01
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	2ivgB02
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	2ivgC01
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	2ivgC02
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	2ivgD01
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	2ivgD02
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	2ivgE01
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	2ivgE02
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	2ivgF01
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	2ivgF02
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	2ivgG01
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	2ivgG02
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	2ivgH01
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	2ivgH02
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	2ivgI01
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	2ivgI02
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	2ivgJ01
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	2ivgJ02
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

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Unit-cell length a length_a	78.392 Å
Unit-cell length b length_b	80.897 Å
Unit-cell length c length_c	81.094 Å
Unit-cell angle α angle_alpha	70.69 °
Unit-cell angle β angle_beta	75.98 °
Unit-cell angle γ angle_gamma	65.15 °
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	1.870 Å
Low-resolution limit resolution_low	76.700 Å
R factor r_factor	0.1470
R_work r_work	0.1450
R_free r_free	0.1880

SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE

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

2ivg__assembly_1__model_1

2ivg__assembly_1__model_1 | I(q)

2ivg__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (2)

SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE

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

2ivg__assembly_1__model_1

2ivg__assembly_1__model_1 | I(q)

2ivg__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (2)