SAXSdb — 1yi8

▼

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

tryptophanyl-tRNA synthetase

Deinococcus radiodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	TRYPTOPHAN × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYW2_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–351； UniProt 21–351 Author chain B； PDBConstruct 21–351； UniProt 21–351 Author chain C； PDBConstruct 21–351； UniProt 21–351

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	1yi8
Deposition date deposition_date	2005-01-11
Structure title title	Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp
Keywords keywords	Auxiliary tryptophanyl trna synthetase, LIGASE; LIGASE
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.

1yi8__assembly_1__model_1

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

Download this curve (.dat)

1yi8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yi8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.71 Å
Rg (electron density)	31.51 Å
Total Rg	31.87 Å
Atom count	5091
Residues	662
Excluded volume	90367 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yi8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yi8__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	tryptophanyl-tRNA synthetase
Molecular weight formula_weight	38225.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C
Atom count atom_count	8661

MPFVDLEVPTMTTPTPAATPARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH

Source Source

Source organism organism	Deinococcus radiodurans
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1059

▼

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1yi8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.0 — automated matches

Domain ID domain_id	d1yi8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.0 — automated matches

Domain ID domain_id	d1yi8c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	1yi8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1yi8A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

Domain ID domain_id	1yi8B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1yi8B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

Domain ID domain_id	1yi8C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1yi8C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

▶

Unit-cell length a length_a	211.800 Å
Unit-cell length b length_b	58.500 Å
Unit-cell length c length_c	88.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2600
R_work r_work	0.2600
R_free r_free	0.2800

Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp

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

tryptophanyl-tRNA synthetase

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

1yi8__assembly_1__model_1

1yi8__assembly_1__model_1 | I(q)

1yi8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp

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

tryptophanyl-tRNA synthetase

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

1yi8__assembly_1__model_1

1yi8__assembly_1__model_1 | I(q)

1yi8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)