3o0n

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin

Method: X-RAY DIFFRACTION

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

Ribonucleoside-diphosphate reductase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THYMIDINE-5'-TRIPHOSPHATE × 2 COBALT (II) ION × 1 CHLORIDE ION × 1 MAGNESIUM ION × 2 COBALAMIN × 1 5'-DEOXYADENOSINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O33839_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–644； UniProt 1–644 Author chain B； PDBConstruct 1–644； UniProt 1–644

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	3o0n
Deposition date deposition_date	2010-07-19
Structure title title	Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin
Keywords keywords	;oxidoreductase, 10 alpha/beta barrel, adenosylcobalamin dependent, ribonucleotide reductase, Reduction ribonucleotide 2'-OH position, EFFECTOR DTTP, COENZYME B12 ;; 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.

3o0n__assembly_1__model_1

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

Download this curve (.dat)

3o0n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3o0n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.30 Å
Rg (electron density)	37.08 Å
Total Rg	37.48 Å
Atom count	9953
Residues	1218
Excluded volume	178610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3o0n__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Ribonucleoside-diphosphate reductase
Molecular weight formula_weight	73374.2 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	A,B
Atom count atom_count	10466

MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGSRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSLQTQVLTKALKT

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	5'-DEOXYADENOSINE
Molecular weight formula_weight	251.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	513

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3o0nA00
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	3o0nB00
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 —

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Unit-cell length a length_a	119.010 Å
Unit-cell length b length_b	123.820 Å
Unit-cell length c length_c	106.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2049
R_work r_work	0.2025
R_free r_free	0.2493

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin

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

Ribonucleoside-diphosphate reductase

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

3o0n__assembly_1__model_1

3o0n__assembly_1__model_1 | I(q)

3o0n__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin

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

Ribonucleoside-diphosphate reductase

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

3o0n__assembly_1__model_1

3o0n__assembly_1__model_1 | I(q)

3o0n__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)