SAXSdb — 3g8q

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

Predicted RNA-binding protein, contains THUMP domain

Methanopyrus kandleri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SODIUM ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SODIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TWU6_METKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 1–278 Author chain B； PDBConstruct 1–278； UniProt 1–278 Author chain C； PDBConstruct 1–278； UniProt 1–278 Author chain D； PDBConstruct 1–278； UniProt 1–278

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	3g8q
Deposition date deposition_date	2009-02-12
Structure title title	A cytidine deaminase edits C-to-U in transfer RNAs in archaea
Keywords keywords	cytidine deaminase, THUMP, ferredoxin-like domain, RNA BINDING PROTEIN; 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.

3g8q__assembly_1__model_1

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

Download this curve (.dat)

3g8q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g8q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.85 Å
Rg (electron density)	26.83 Å
Total Rg	27.50 Å
Atom count	4305
Residues	555
Excluded volume	76732 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g8q__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3g8q__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Predicted RNA-binding protein, contains THUMP domain
Molecular weight formula_weight	30657.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8787

MKVSLAGQTVDVKKILNEIPKRTVTAALLEGGEIVAVEEADDEHAERKLVRRHDVEGKVVFVTARPCLYCARELAEAGVAGVVYLGRGRGLGPYYLARSGVEVVEVHPDEPLGYDPVDRLDVLLTFGGNPYLTEEDVAARVYCLLTGRGFDADIAPAPENLSGRVEIMVTRGDPDEAVELLKEELPVFRIRRFLISGEFDRDELRERILEDIEPRILDPFAVRARIARAGAFSSSREAEVFIGDVLTSVGREVNLNDPRTVVTVDVLGPRVSVGVEKR

Source Source

Source organism organism	Methanopyrus kandleri
NCBI taxonomy ID ncbi_taxonomy_id	2320
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	189

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3g8qA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3g8qA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1940 —

Domain ID domain_id	3g8qA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

Domain ID domain_id	3g8qB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3g8qB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1940 —

Domain ID domain_id	3g8qB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

Domain ID domain_id	3g8qC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3g8qC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1940 —

Domain ID domain_id	3g8qC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

Domain ID domain_id	3g8qD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	3g8qD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1940 —

Domain ID domain_id	3g8qD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2300 — THUMP fold
Homologous superfamily homologous superfamily	10 — THUMP superfamily

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Unit-cell length a length_a	184.465 Å
Unit-cell length b length_b	77.060 Å
Unit-cell length c length_c	109.082 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2050
R_work r_work	0.2018
R_free r_free	0.2648

A cytidine deaminase edits C-to-U in transfer RNAs in archaea

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

Predicted RNA-binding protein, contains THUMP domain

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

3g8q__assembly_1__model_1

3g8q__assembly_1__model_1 | I(q)

3g8q__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

A cytidine deaminase edits C-to-U in transfer RNAs in archaea

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

Predicted RNA-binding protein, contains THUMP domain

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

3g8q__assembly_1__model_1

3g8q__assembly_1__model_1 | I(q)

3g8q__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)