1ryz

Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution

Method: X-RAY DIFFRACTION

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

Uridine phosphorylase

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ACETIC ACID × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	ACETIC ACID × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ACETIC ACID × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UDP_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 0–252 Author chain B； PDBConstruct 1–253； UniProt 0–252 Author chain C； PDBConstruct 1–253； UniProt 0–252 Author chain D； PDBConstruct 1–253； UniProt 0–252 Author chain E； PDBConstruct 1–253； UniProt 0–252 Author chain F； PDBConstruct 1–253； UniProt 0–252

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	1ryz
Deposition date deposition_date	2003-12-23
Structure title title	Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution
Keywords keywords	uridine phosphorylase, nucleoside phosphorylase, TRANSFERASE; TRANSFERASE
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.

1ryz__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ryz__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ryz__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	23.51 Å
Rg (electron density)	22.54 Å
Total Rg	23.40 Å
Atom count	3754
Residues	500
Excluded volume	66844 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ryz__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ryz__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ryz__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ryz__assembly_4__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1ryza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1ryzb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1ryzc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1ryzd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1ryze_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1ryzf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (6 domains)

Domain ID domain_id	1ryzA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1ryzB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1ryzC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1ryzD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1ryzE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1ryzF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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Unit-cell length a length_a	92.260 Å
Unit-cell length b length_b	92.260 Å
Unit-cell length c length_c	267.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	29.460 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2840

Description description	Uridine phosphorylase
Molecular weight formula_weight	27169.1 kDa
EC 编号 ec_number	2.4.2.3
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11270

Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution

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

Uridine phosphorylase

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

1ryz__assembly_4__model_1

1ryz__assembly_4__model_1 | I(q)

1ryz__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution

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

Uridine phosphorylase

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

1ryz__assembly_4__model_1

1ryz__assembly_4__model_1 | I(q)

1ryz__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)