1ynf

Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli

Method: X-RAY DIFFRACTION

▼

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

Succinylarginine dihydrolase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	POTASSIUM ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	POTASSIUM ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	POTASSIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASTB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–458； UniProt 2–447 Author chain B； PDBConstruct 13–458； UniProt 2–447 Author chain C； PDBConstruct 13–458； UniProt 2–447 Author chain D； PDBConstruct 13–458； UniProt 2–447 Author chain E； PDBConstruct 13–458； UniProt 2–447 Author chain F； PDBConstruct 13–458； UniProt 2–447

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	1ynf
Deposition date deposition_date	2005-01-24
Structure title title	Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli
Keywords keywords	Succinylarginine, Dihydrolase, HYDROLASE; HYDROLASE
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.

1ynf__assembly_1__model_1

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

Download this curve (.dat)

1ynf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ynf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.32 Å
Rg (electron density)	29.45 Å
Total Rg	30.30 Å
Atom count	6708
Residues	840
Excluded volume	118490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ynf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ynf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ynf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Succinylarginine dihydrolase
Molecular weight formula_weight	50977.6 kDa
EC 编号 ec_number	3.-.-.-
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	21526

MGSSHHHHHHGSNAWEVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQAVIPPHERPFIPVLRQLGFSGSDEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADTLDGKVHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFSVHSALPQVALLGDEGAANHNRLGGHYGEPGMQLFVYGREEGNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQNPDVIDQGVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGFMAIEVPATQVSVSDTVSTYLFNSQLLSRDDGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANGGGPACLRLRVVLTEEERRAVNPAVMMNDTLFNALNDWVDRYYRDRLTAADLADPQLLREGREALDVLSQLLNLGSVYPFQREGGGNG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1402

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1ynfa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

Domain ID domain_id	d1ynfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

Domain ID domain_id	d1ynfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

Domain ID domain_id	d1ynfd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

Domain ID domain_id	d1ynfe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

Domain ID domain_id	d1ynff_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.7 — Succinylarginine dihydrolase-like

CATH v4.4 (6 domains)

Domain ID domain_id	1ynfA00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

Domain ID domain_id	1ynfB00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

Domain ID domain_id	1ynfC00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

Domain ID domain_id	1ynfD00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

Domain ID domain_id	1ynfE00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

Domain ID domain_id	1ynfF00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	20 — Succinylarginine dihydrolase

▶

Unit-cell length a length_a	55.834 Å
Unit-cell length b length_b	94.172 Å
Unit-cell length c length_c	139.660 Å
Unit-cell angle α angle_alpha	75.41 °
Unit-cell angle β angle_beta	78.38 °
Unit-cell angle γ angle_gamma	89.74 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	27.320 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2520

Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli

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

Succinylarginine dihydrolase

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

1ynf__assembly_1__model_1

1ynf__assembly_1__model_1 | I(q)

1ynf__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli

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

Succinylarginine dihydrolase

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

1ynf__assembly_1__model_1

1ynf__assembly_1__model_1 | I(q)

1ynf__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)