2bq1

Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium

Method: X-RAY DIFFRACTION

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

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT

SALMONELLA TYPHIMURIUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT × 2 （P17424） 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 FE (III) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIR3_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 2–714； UniProt 1–713 Author chain F； PDBConstruct 2–714； UniProt 1–713

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT

SALMONELLA TYPHIMURIUM

UniProt P17424

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT × 2 （Q08698） 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 FE (III) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIR4_SALTY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–319； UniProt 1–319 Author chain J； PDBConstruct 1–319； UniProt 1–319

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	2bq1
Deposition date deposition_date	2005-04-26
Structure title title	Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
Keywords keywords	;R1, R2, R1E, R2F, IRON, CLASS 1B, HOLOCOMPLEX, ALLOSTERIC REGULATION, RIBONUCLEOTIDE REDUCTASE, ATP-BINDING, METAL-BINDING, OXIDOREDUCTASE, DNA REPLICATION, RADICAL TRANSFER, ALLOSTERIC ENZYME, ASYMMETRIC COMPLEX, NUCLEOTIDE-BINDING ;; OXIDOREDUCTASE
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.

2bq1__assembly_1__model_1

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

Download this curve (.dat)

2bq1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bq1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.01 Å
Rg (electron density)	42.50 Å
Total Rg	42.80 Å
Atom count	15520
Residues	1936
Excluded volume	275670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bq1__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	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT
Molecular weight formula_weight	80686.2 kDa
EC 编号 ec_number	1.17.4.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F
Atom count atom_count	15520

MATTTPERVMQETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQHERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFLLRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLEDAFSYANQLGARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFRLAKENAQMALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLAEIQFESGYPYIMFEDTVNRANPIAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVETAIRGLTAVSDMSHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHTSMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFMTNENLDMYQDAYDIGPEKIIDTYAEATRHVDQGLSLTLFFPDTATTRDINKAQIYAWRKGIKSLYYIRLRQLALEGTEIEGCVSCAL

Source Source

Source organism organism	SALMONELLA TYPHIMURIUM
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT
Molecular weight formula_weight	36263.0 kDa
EC 编号 ec_number	1.17.4.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

MKLSRISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENHDFFSGSGSSYVMGKTVETEDEDWNF

Source Source

Source organism organism	SALMONELLA TYPHIMURIUM
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2bq1e1
Class class	a — All alpha proteins
Fold Fold fold	a.98 — R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily Superfamily superfamily	a.98.1 — R1 subunit of ribonucleotide reductase, N-terminal domain
Family Family family	a.98.1.1 — R1 subunit of ribonucleotide reductase, N-terminal domain

Domain ID domain_id	d2bq1e2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.2 — R1 subunit of ribonucleotide reductase, C-terminal domain

Domain ID domain_id	d2bq1f1
Class class	a — All alpha proteins
Fold Fold fold	a.98 — R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily Superfamily superfamily	a.98.1 — R1 subunit of ribonucleotide reductase, N-terminal domain
Family Family family	a.98.1.1 — R1 subunit of ribonucleotide reductase, N-terminal domain

Domain ID domain_id	d2bq1f2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.2 — R1 subunit of ribonucleotide reductase, C-terminal domain

Domain ID domain_id	d2bq1i1
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.2 — Ribonucleotide reductase-like

Domain ID domain_id	d2bq1j1
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.2 — Ribonucleotide reductase-like

CATH v4.4 (6 domains)

Domain ID domain_id	2bq1E02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bq1E03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1650 — 50s Ribosomal Protein L19e, Chain O, domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bq1F02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bq1F03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1650 — 50s Ribosomal Protein L19e, Chain O, domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bq1I01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	2bq1J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

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Unit-cell length a length_a	270.372 Å
Unit-cell length b length_b	270.372 Å
Unit-cell length c length_c	270.372 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	3.990 Å
Low-resolution limit resolution_low	182.570 Å
R factor r_factor	0.2650
R_work r_work	0.2620
R_free r_free	0.3100

Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium

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

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT

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

2bq1__assembly_1__model_1

2bq1__assembly_1__model_1 | I(q)

2bq1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium

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

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT

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

2bq1__assembly_1__model_1

2bq1__assembly_1__model_1 | I(q)

2bq1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)