2rcc

Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution

Method: X-RAY DIFFRACTION

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

Ribonucleoside-diphosphate reductase subunit beta

Bacillus halodurans C-125

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	TETRAETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 3 ZINC ION × 2 1,2-ETHANEDIOL × 1 TRIETHYLENE GLYCOL × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DI(HYDROXYETHYL)ETHER × 6 ZINC ION × 4 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	TETRAETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 12 ZINC ION × 8 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 2 GLYCEROL × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIR2_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–346； UniProt 1–345 Author chain B； PDBConstruct 2–346； UniProt 1–345 Author chain C； PDBConstruct 2–346； UniProt 1–345

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	2rcc
Deposition date deposition_date	2007-09-19
Structure title title	Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution
Keywords keywords	;NP_241368.1, Putative Class I Ribonucleotide Reductase, Ribonucleotide reductase, small chain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, DNA replication, Iron, Metal-binding, Oxidoreductase ;; 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.

2rcc__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2rcc__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rcc__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	45.18 Å
Rg (electron density)	45.58 Å
Total Rg	45.63 Å
Atom count	14816
Residues	1746
Excluded volume	266550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rcc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rcc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2rcc__assembly_3__model_1`	hexameric （6）	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 (8)

Entity 1 Entity 1 polymer

Description description	Ribonucleoside-diphosphate reductase subunit beta
Molecular weight formula_weight	40855.3 kDa
EC 编号 ec_number	1.17.4.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7885

GMEQLQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSMRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIRAYEDVNSGKSDFFEQKSRQYAKVSADNGFDEL

Source Source

Source organism organism	Bacillus halodurans C-125
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2rccb_
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.25.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2rccA01
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	2rccB01
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	2rccC01
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	175.260 Å
Unit-cell length b length_b	72.780 Å
Unit-cell length c length_c	111.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	28.502 Å
R factor r_factor	0.1840
R_work r_work	0.1830
R_free r_free	0.2150

Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution

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

Ribonucleoside-diphosphate reductase subunit beta

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

2rcc__assembly_3__model_1

2rcc__assembly_3__model_1 | I(q)

2rcc__assembly_3__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution

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

Ribonucleoside-diphosphate reductase subunit beta

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

2rcc__assembly_3__model_1

2rcc__assembly_3__model_1 | I(q)

2rcc__assembly_3__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)