SAXSdb — 1u7x

▼

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

Tyrosyl-tRNA synthetase

Methanocaldococcus jannaschii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYY_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 1–306 Author chain B； PDBConstruct 1–306； UniProt 1–306

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	1u7x
Deposition date deposition_date	2004-08-04
Structure title title	crystal structure of a mutant M. jannashii tyrosyl-tRNA synthetase specific for O-methyl-tyrosine
Keywords keywords	Rossmann fold, 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.

1u7x__assembly_1__model_1

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

Download this curve (.dat)

1u7x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u7x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.70 Å
Rg (electron density)	33.89 Å
Total Rg	34.12 Å
Atom count	4888
Residues	612
Excluded volume	88375 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u7x__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 (2)

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1u7xa_
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.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Domain ID domain_id	d1u7xb_
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.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1u7xA01
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	1u7xA02
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	1u7xB01
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	1u7xB02
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	45.371 Å
Unit-cell length b length_b	185.000 Å
Unit-cell length c length_c	93.765 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	46.250 Å
R factor r_factor	0.2370
R_work r_work	0.2290
R_free r_free	0.3080

Description description	Tyrosyl-tRNA synthetase
Molecular weight formula_weight	35808.6 kDa
EC 编号 ec_number	6.1.1.1
Mutation mutation	A158D, Q32Y, R107E, P162L
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4888

crystal structure of a mutant M. jannashii tyrosyl-tRNA synthetase specific for O-methyl-tyrosine

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

Tyrosyl-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

1u7x__assembly_1__model_1

1u7x__assembly_1__model_1 | I(q)

1u7x__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

crystal structure of a mutant M. jannashii tyrosyl-tRNA synthetase specific for O-methyl-tyrosine

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

Tyrosyl-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

1u7x__assembly_1__model_1

1u7x__assembly_1__model_1 | I(q)

1u7x__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)