SAXSdb — 3ee4

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

Probable ribonucleoside-diphosphate reductase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MYRISTIC ACID × 2 MANGANESE (III) ION × 2 FE (III) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P96416_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–323； UniProt 1–314

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	3ee4
Deposition date deposition_date	2008-09-04
Structure title title	R2-like ligand binding Mn/Fe oxidase from M. tuberculosis
Keywords keywords	manganese, iron, diiron, carboxylate, oxidase, R2, ligand, cavity, monooxygenase, 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.

3ee4__assembly_1__model_1

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

Download this curve (.dat)

3ee4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ee4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.83 Å
Rg (electron density)	24.95 Å
Total Rg	25.63 Å
Atom count	4674
Residues	578
Excluded volume	82552 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ee4__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 (5)

Entity 1 Entity 1 polymer

Description description	Probable ribonucleoside-diphosphate reductase
Molecular weight formula_weight	36785.2 kDa
EC 编号 ec_number	1.17.4.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2604

MAHHHHHHGMTRTRSGSLAAGGLNWASLPLKLFAGGNAKFWHPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDVDYSPAQLEDTFADEDRRTLAAASA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (III) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 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	267

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3ee4A00
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	54.565 Å
Unit-cell length b length_b	54.565 Å
Unit-cell length c length_c	176.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.850 Å
R factor r_factor	0.1500
R_work r_work	0.1485
R_free r_free	0.1769

R2-like ligand binding Mn/Fe oxidase from M. tuberculosis

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

Probable 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

3ee4__assembly_1__model_1

3ee4__assembly_1__model_1 | I(q)

3ee4__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

R2-like ligand binding Mn/Fe oxidase from M. tuberculosis

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

Probable 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

3ee4__assembly_1__model_1

3ee4__assembly_1__model_1 | I(q)

3ee4__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)