SAXSdb — 3b9x

▼

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

Pyrimidine-specific ribonucleoside hydrolase rihB

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	CALCIUM ION × 4 INOSINE × 4 TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIHB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–333； UniProt 1–313 Author chain B； PDBConstruct 21–333； UniProt 1–313 Author chain C； PDBConstruct 21–333； UniProt 1–313 Author chain D； PDBConstruct 21–333； UniProt 1–313

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	3b9x
Deposition date deposition_date	2007-11-07
Structure title title	Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine
Keywords keywords	Open (alpha, beta) structure, NH-fold, enzyme-substrate complex, protein-nucleoside complex, Glycosidase, Hydrolase, Metal-binding; 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.

3b9x__assembly_1__model_1

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

Download this curve (.dat)

3b9x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b9x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.85 Å
Rg (electron density)	34.25 Å
Total Rg	34.70 Å
Atom count	9121
Residues	1202
Excluded volume	163810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b9x__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Pyrimidine-specific ribonucleoside hydrolase rihB
Molecular weight formula_weight	35933.2 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	9468

MGSSHHHHHHSSGLVPRGSHMEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIKTH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	INOSINE
Molecular weight formula_weight	268.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 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	331

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3b9xa_
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	d3b9xb_
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	d3b9xc_
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	d3b9xd_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3b9xA00
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	3b9xB00
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	3b9xC00
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	3b9xD00
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

▶

Unit-cell length a length_a	45.112 Å
Unit-cell length b length_b	82.406 Å
Unit-cell length c length_c	90.163 Å
Unit-cell angle α angle_alpha	67.90 °
Unit-cell angle β angle_beta	79.59 °
Unit-cell angle γ angle_gamma	89.65 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	81.920 Å
R factor r_factor	0.2030
R_work r_work	0.2010
R_free r_free	0.2550

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

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

Pyrimidine-specific ribonucleoside hydrolase rihB

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

3b9x__assembly_1__model_1

3b9x__assembly_1__model_1 | I(q)

3b9x__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

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

Pyrimidine-specific ribonucleoside hydrolase rihB

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

3b9x__assembly_1__model_1

3b9x__assembly_1__model_1 | I(q)

3b9x__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)