SAXSdb — 3g5i

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

Pyrimidine-specific ribonucleoside hydrolase rihA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	BETA-MERCAPTOETHANOL × 1 CALCIUM ION × 4 (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIHA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–312； UniProt 2–311 Author chain B； PDBConstruct 3–312； UniProt 2–311 Author chain C； PDBConstruct 3–312； UniProt 2–311 Author chain D； PDBConstruct 3–312； UniProt 2–311

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	3g5i
Deposition date deposition_date	2009-02-05
Structure title title	Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
Keywords keywords	Open (alpha, beta) structure, Glycosidase, Hydrolase; HYDROLASE
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.

3g5i__assembly_1__model_1

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

Download this curve (.dat)

3g5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g5i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.82 Å
Rg (electron density)	34.31 Å
Total Rg	34.80 Å
Atom count	9190
Residues	1197
Excluded volume	165310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g5i__assembly_1__model_1`	tetrameric （4）	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	Pyrimidine-specific ribonucleoside hydrolase rihA
Molecular weight formula_weight	33866.7 kDa
EC 编号 ec_number	3.2.2.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9716

GSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	(2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol
Molecular weight formula_weight	239.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	510

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3g5ia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.70 — Nucleoside hydrolase
Superfamily Superfamily superfamily	c.70.1 — Nucleoside hydrolase
Family Family family	c.70.1.0 — automated matches

Domain ID domain_id	d3g5ib1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.70 — Nucleoside hydrolase
Superfamily Superfamily superfamily	c.70.1 — Nucleoside hydrolase
Family Family family	c.70.1.0 — automated matches

Domain ID domain_id	d3g5ib2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3g5ic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.70 — Nucleoside hydrolase
Superfamily Superfamily superfamily	c.70.1 — Nucleoside hydrolase
Family Family family	c.70.1.0 — automated matches

Domain ID domain_id	d3g5id1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.70 — Nucleoside hydrolase
Superfamily Superfamily superfamily	c.70.1 — Nucleoside hydrolase
Family Family family	c.70.1.0 — automated matches

Domain ID domain_id	d3g5id2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3g5iA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

Domain ID domain_id	3g5iB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

Domain ID domain_id	3g5iC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

Domain ID domain_id	3g5iD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

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Unit-cell length a length_a	84.350 Å
Unit-cell length b length_b	82.910 Å
Unit-cell length c length_c	93.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	37.500 Å
R factor r_factor	0.2048
R_work r_work	0.2029
R_free r_free	0.2409

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

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

Pyrimidine-specific ribonucleoside hydrolase rihA

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

3g5i__assembly_1__model_1

3g5i__assembly_1__model_1 | I(q)

3g5i__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

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

Pyrimidine-specific ribonucleoside hydrolase rihA

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

3g5i__assembly_1__model_1

3g5i__assembly_1__model_1 | I(q)

3g5i__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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (3)