1it8

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

Method: X-RAY DIFFRACTION

▼

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

archaeosine tRNA-guanine transglycosylase

Pyrococcus horikoshii

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 MAGNESIUM ION × 2 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58843_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–582； UniProt 1–582 Author chain B； PDBConstruct 1–582； UniProt 1–582

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1it8
Deposition date deposition_date	2002-01-11
Structure title title	Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0
Keywords keywords	(alpha/beta)8 barrel, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1it8__assembly_1__model_1

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

Download this curve (.dat)

1it8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1it8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.15 Å
Rg (electron density)	33.39 Å
Total Rg	33.99 Å
Atom count	9321
Residues	1154
Excluded volume	167260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1it8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	archaeosine tRNA-guanine transglycosylase
Molecular weight formula_weight	66700.1 kDa
EC 编号 ec_number	2.4.2.29
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	9463

MSRGDKMLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE
Molecular weight formula_weight	175.1 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	142

▼

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1it8a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
Family Family family	c.1.20.1 — tRNA-guanine transglycosylase

Domain ID domain_id	d1it8a3
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d1it8a4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.6 — Pre-PUA domain
Family Family family	d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain

Domain ID domain_id	d1it8b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
Family Family family	c.1.20.1 — tRNA-guanine transglycosylase

Domain ID domain_id	d1it8b3
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d1it8b4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.6 — Pre-PUA domain
Family Family family	d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain

CATH v4.4 (8 domains)

Domain ID domain_id	1it8A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

Domain ID domain_id	1it8A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — ArcTGT, C1 domain

Domain ID domain_id	1it8A03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	90 — ArcTGT, C2 domain

Domain ID domain_id	1it8A04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	10 — PUA domain

Domain ID domain_id	1it8B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

Domain ID domain_id	1it8B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — ArcTGT, C1 domain

Domain ID domain_id	1it8B03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	90 — ArcTGT, C2 domain

Domain ID domain_id	1it8B04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	10 — PUA domain

▶

Unit-cell length a length_a	100.467 Å
Unit-cell length b length_b	100.467 Å
Unit-cell length c length_c	366.168 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	34.870 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2780

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

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

archaeosine tRNA-guanine transglycosylase

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

1it8__assembly_1__model_1

1it8__assembly_1__model_1 | I(q)

1it8__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

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

archaeosine tRNA-guanine transglycosylase

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

1it8__assembly_1__model_1

1it8__assembly_1__model_1 | I(q)

1it8__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)