9by0

Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex

Method: ELECTRON MICROSCOPY

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

Ribonucleoside-diphosphate reductase subunit alpha

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ribonucleoside-diphosphate reductase subunit beta × 2 （P50621） Thioredoxin × 1 （P14949） THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 GUANOSINE-5'-DIPHOSPHATE × 2 MANGANESE (II) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIR1_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–700； UniProt 1–700 Author chain B； PDBConstruct 1–700； UniProt 1–700

Ribonucleoside-diphosphate reductase subunit beta

Bacillus subtilis

UniProt P50621

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ribonucleoside-diphosphate reductase subunit alpha × 2 （P50620） Thioredoxin × 1 （P14949） THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 GUANOSINE-5'-DIPHOSPHATE × 2 MANGANESE (II) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIR2_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 22–350； UniProt 1–329 Author chain D； PDBConstruct 22–350； UniProt 1–329

Thioredoxin

Bacillus subtilis

UniProt P14949

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ribonucleoside-diphosphate reductase subunit alpha × 2 （P50620） Ribonucleoside-diphosphate reductase subunit beta × 2 （P50621） THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 GUANOSINE-5'-DIPHOSPHATE × 2 MANGANESE (II) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIO_BACSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–104； UniProt 1–104

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	9by0
Deposition date deposition_date	2024-05-23
Structure title title	Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex
Keywords keywords	Ribonucleotide Reductase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9by0__assembly_1__model_1

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

Download this curve (.dat)

9by0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9by0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.39 Å
Rg (electron density)	41.81 Å
Total Rg	42.07 Å
Atom count	16678
Residues	2026
Excluded volume	297160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9by0__assembly_1__model_1`	pentameric （5）	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 alpha
Molecular weight formula_weight	80791.5 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	16678

MSQNQVPKWIQLNNEIMIQKDGKFQFDKDKEAVHSYFVDYINQNTVFFHNLKEKLDYLVENQYYEEEFLSLYSFEDIKEVFKTAYAKKFRFPSFMSAFKFYNDYALKTNDKKKILERYEDRISIVALFFANGDTEKAKEYVNLMINQEYQPSTPTFLNAGRKRRGELVSCFLLEVNDSLNDISRAIDISMQLSKLGGGVSLNLSKLRAKGEAIKDVENATKGVVGVMKLLDNAFRYADQMGQRQGSGAAYLNIFHRDINDFLDTKKISADEDVRVKTLSIGVVIPDKFVELAREDKAAYVFYPHTIYKEYGQHMDEMDMNEMYDKFVDNPRVKKEKINPRKLLEKLAMLRSESGYPYIMFQDNVNKVHANNHISKVKFSNLCSEVLQASQVSSYTDYDEEDEIGLDISCNLGSLNILNVMEHKSIEKTVKLATDSLTHVSETTDIRNAPAVRRANKAMKSIGLGAMNLHGYLAQNGIAYESPEARDFANTFFMMVNFYSIQRSAEIAKEKGETFDQYEGSTYATGEYFDKYVSTDFSPKYEKIANLFEGMHIPTTEDWKKLKAFVAEHGMYHSYRLCIAPTGSISYVQSSTASVMPIMERIEERTYGNSKTYYPMPGLASNNWFFYKEAYDMDMFKVVDMIATIQQHIDQGISFTLFLKDTMTTRDLNRIDLYAHHRGIKTIYYARTKDTGQDSCLSCVV

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribonucleoside-diphosphate reductase subunit beta
Molecular weight formula_weight	40721.0 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	C,D

MGSSHHHHHHSSGLVPRGSHMMTKIYDAANWSKHEDDFTQMFYNQNVKQFWLPEEIALNGDLLTWKYLGKNEQDTYMKVLAGLTLLDTEQGNTGMPIVAEHVDGHQRKAVLNFMAMMENAVHAKSYSNIFMTLAPTETINEVFEWVKQNKYLQKKAQMIVGLYKAIQKDDEISLFKAMVASVYLESFLFYSGFYYPLYFYGQGKLMQSGEIINLILRDEAIHGVYVGLLAQEIYNKQTEEKKAELREFAIDLLNQLYENELEYTEDLYDQVGLSHDVKKFIRYNANKALMNLGFDPYFEEEDINPIVLNGLNTKTKSHDFFSMKGNGYKKATVEPLKDDDFYFEDEKEQI

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Thioredoxin
Molecular weight formula_weight	11404.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAIVKATDQSFSAETSEGVVLADFWAPWCGPCKMIAPVLEELDQEMGDKLKIVKIDVDENQETAGKYGVMSIPTLLVLKDGEVVETSVGFKPKEALQELVNKHL

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 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 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	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

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Resolution resolution	4.19 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	36000

Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex

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

Ribonucleoside-diphosphate reductase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Ribonucleoside-diphosphate reductase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Thioredoxin

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

9by0__assembly_1__model_1

9by0__assembly_1__model_1 | I(q)

9by0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

7. Citations (1)

Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex

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

Ribonucleoside-diphosphate reductase subunit alpha

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 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

Thioredoxin

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

9by0__assembly_1__model_1

9by0__assembly_1__model_1 | I(q)

9by0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

7. Citations (1)