SAXSdb — 8dcg

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

tRNA-splicing ligase RtcB

Pyrococcus horikoshii OT3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 GUANOSINE-5'-MONOPHOSPHATE × 1 SULFATE ION × 13 CHLORIDE ION × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 GUANOSINE-5'-MONOPHOSPHATE × 1 SULFATE ION × 12 CHLORIDE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RTCB_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–116； UniProt 1–96 Author chain A； PDBConstruct 117–501； UniProt 487–871 Author chain B； PDBConstruct 21–116； UniProt 1–96 Author chain B； PDBConstruct 117–501； UniProt 487–871

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	8dcg
Deposition date deposition_date	2022-06-16
Structure title title	Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii
Keywords keywords	RNA ligase, RtcB, RtcB-GMP, guanylylation, tRNA splicing, RNA repair, LIGASE; LIGASE
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.

8dcg__assembly_1__model_1

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

Download this curve (.dat)

8dcg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dcg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.45 Å
Rg (electron density)	21.49 Å
Total Rg	22.41 Å
Atom count	3880
Residues	481
Excluded volume	68423 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dcg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8dcg__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	tRNA-splicing ligase RtcB
Molecular weight formula_weight	55753.8 kDa
EC 编号 ec_number	6.5.1.8,6.5.1.8
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	7850

MGSSHHHHHHSSGLVPRGSHMVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG

Source Source

Source organism organism	Pyrococcus horikoshii OT3
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8dcgB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1860 — tRNA-splicing ligase RtcB
Homologous superfamily homologous superfamily	10 — tRNA-splicing ligase RtcB

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Unit-cell length a length_a	143.560 Å
Unit-cell length b length_b	143.560 Å
Unit-cell length c length_c	80.301 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	tetragonal

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	47.850 Å
R factor r_factor	0.1918
R_work r_work	0.1905
R_free r_free	0.2168

Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii

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

tRNA-splicing ligase RtcB

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

8dcg__assembly_1__model_1

8dcg__assembly_1__model_1 | I(q)

8dcg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii

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

tRNA-splicing ligase RtcB

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

8dcg__assembly_1__model_1

8dcg__assembly_1__model_1 | I(q)

8dcg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)