SAXSdb — 2b56

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

RNA editing complex protein MP57

Trypanosoma brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ;URIDINE 5'-TRIPHOSPHATE ; × 1 URIDINE-5'-MONOPHOSPHATE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q86MV5_9TRYP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–468； UniProt 20–487

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	2b56
Deposition date deposition_date	2005-09-27
Structure title title	Structural Basis for UTP Specificity of RNA Editing TUTases From Trypanosoma Brucei
Keywords keywords	TbRET2, TUTase, RNA Editing, transferase, trypanosoma brucei, TRANSFERASE-RNA BINDING PROTEIN COMPLEX; TRANSFERASE/RNA BINDING PROTEIN
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.

2b56__assembly_1__model_1

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

Download this curve (.dat)

2b56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.33 Å
Rg (electron density)	24.66 Å
Total Rg	25.31 Å
Atom count	3637
Residues	444
Excluded volume	64095 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b56__assembly_1__model_1`	monomeric （1）	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	RNA editing complex protein MP57
Molecular weight formula_weight	54142.7 kDa
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	3917

SPLSLPSTKLNPSPDHYAVWGKAIMAENNRRVGPEHMFRTAIRAQQQLQGLADKWTPDAKVYCCGSMVTYGQMERGSDLDLACMFDDPYPSHEVQAKRTDKLRTVIKRYVPHYLRNNLLGLTEARTPVVKLRFANDEKVARARYTPLSEEEDRKARTALLDVRNQCVGDNDVEYIAEKMGRDNVEGIRVDRTTYGCRIAIQCTSKEQMIEAIGFFPDGKIMTRGMREDYTRDVLDVRFVPEMFMYRWDISFVGYGVKNSYLIRHYLHNGPVAARHTAMAVKAWGKATNVGAGSGAMLTSYAVTVMFIYYLLVTRQVLWVDPWSLPHPAHLPRYPDFSPLYDCDPTELGRLLHGFFIFYAHHFDYEREVVSLNRNRRSYRSDIGWNFPQNKKGTFSYNFCIEDPYEDVGTGGLNLVRHLHPAKFQLVKQEFLRAAQCMERFLPTNAPEKSILGVKRADLRHFERDRDRE

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2b56a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.10 — RNA editing terminal uridyl transferase 2, RET2, catalytic domain

Domain ID domain_id	d2b56a2
Class class	a — All alpha proteins
Fold Fold fold	a.160 — PAP/OAS1 substrate-binding domain
Superfamily Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
Family Family family	a.160.1.4 — RNA editing terminal uridyl transferase 2, RET2, domain 2

CATH v4.4 (3 domains)

Domain ID domain_id	2b56A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1410 — Poly(a)-polymerase, middle domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2b56A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2b56A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1970 —

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Unit-cell length a length_a	91.435 Å
Unit-cell length b length_b	91.435 Å
Unit-cell length c length_c	162.529 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1940
R_work r_work	0.1925
R_free r_free	0.2209

Structural Basis for UTP Specificity of RNA Editing TUTases From Trypanosoma Brucei

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

RNA editing complex protein MP57

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

2b56__assembly_1__model_1

2b56__assembly_1__model_1 | I(q)

2b56__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structural Basis for UTP Specificity of RNA Editing TUTases From Trypanosoma Brucei

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

RNA editing complex protein MP57

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

2b56__assembly_1__model_1

2b56__assembly_1__model_1 | I(q)

2b56__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)