SAXSdb — 2j5b

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

TYROSYL-TRNA SYNTHETASE

ACANTHAMOEBA POLYPHAGA MIMIVIRUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-[(2S)-2-amino-3-hydroxypropyl]phenol × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYY_MIMIV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–348； UniProt 2–346 Author chain B； PDBConstruct 4–348； UniProt 2–346

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	2j5b
Deposition date deposition_date	2006-09-13
Structure title title	Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol
Keywords keywords	LIGASE, PROTEIN BIOSYNTHESIS, ATP-BINDING; 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.

2j5b__assembly_1__model_1

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

Download this curve (.dat)

2j5b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j5b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.81 Å
Rg (electron density)	32.44 Å
Total Rg	32.86 Å
Atom count	5193
Residues	643
Excluded volume	92971 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j5b__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	TYROSYL-TRNA SYNTHETASE
Molecular weight formula_weight	39895.7 kDa
EC 编号 ec_number	6.1.1.1
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	5523

AGLENTDHTNNEHRLTQLLSIAEECETLDRLKQLVDSGRIFTAYNGFEPSGRIHIAQALITVMNTNNMIECGGQMIIYIADWFAKMNLKMNGDINKIRELGRYFIEVFKACGINLDGTRFIWASEFIASNPSYIERMLDIAEFSTISRVKRCCQIMGRNESDCLKASQIFYPCMQAADVFELVPEGIDICQLGIDQRKVNMLAIEYANDRGLKIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDDTEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGKIYTDIESIQEDFSSMNKRELKTDVANYINTIIDLVREHFKKPELSELLSNVKSYQQPSK

Source Source

Source organism organism	ACANTHAMOEBA POLYPHAGA MIMIVIRUS
NCBI taxonomy ID ncbi_taxonomy_id	212035
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	4-[(2S)-2-amino-3-hydroxypropyl]phenol
Molecular weight formula_weight	167.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	330

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2j5bA01
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	2j5bA02
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	2j5bB01
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	2j5bB02
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

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Unit-cell length a length_a	63.502 Å
Unit-cell length b length_b	107.300 Å
Unit-cell length c length_c	148.890 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	2.200 Å
Low-resolution limit resolution_low	29.830 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2480

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol

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

2j5b__assembly_1__model_1

2j5b__assembly_1__model_1 | I(q)

2j5b__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol

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

2j5b__assembly_1__model_1

2j5b__assembly_1__model_1 | I(q)

2j5b__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)