2e21

Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.

Method: X-RAY DIFFRACTION

▼

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

tRNA(Ile)-lysidine synthase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TILS_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317 Author chain C； PDBConstruct 1–317； UniProt 1–317 Author chain D； PDBConstruct 1–317； UniProt 1–317

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	2e21
Deposition date deposition_date	2006-11-06
Structure title title	Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.
Keywords keywords	;Rossmann-fold, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2e21__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2e21__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2e21__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.12 Å
Rg (electron density)	28.11 Å
Total Rg	28.93 Å
Atom count	5243
Residues	628
Excluded volume	94236 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2e21__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2e21__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	tRNA(Ile)-lysidine synthase
Molecular weight formula_weight	37389.5 kDa
EC 编号 ec_number	6.3.4.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10690

MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFSPEV

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 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	180

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2e21a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.5 — PP-loop ATPase

Domain ID domain_id	d2e21a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.229 — MesJ substrate recognition domain-like
Superfamily Superfamily superfamily	d.229.1 — MesJ substrate recognition domain-like
Family Family family	d.229.1.1 — MesJ substrate recognition domain-like

Domain ID domain_id	d2e21b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.5 — PP-loop ATPase

Domain ID domain_id	d2e21b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.229 — MesJ substrate recognition domain-like
Superfamily Superfamily superfamily	d.229.1 — MesJ substrate recognition domain-like
Family Family family	d.229.1.1 — MesJ substrate recognition domain-like

Domain ID domain_id	d2e21c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.5 — PP-loop ATPase

Domain ID domain_id	d2e21c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.229 — MesJ substrate recognition domain-like
Superfamily Superfamily superfamily	d.229.1 — MesJ substrate recognition domain-like
Family Family family	d.229.1.1 — MesJ substrate recognition domain-like

Domain ID domain_id	d2e21d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.5 — PP-loop ATPase

Domain ID domain_id	d2e21d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.229 — MesJ substrate recognition domain-like
Superfamily Superfamily superfamily	d.229.1 — MesJ substrate recognition domain-like
Family Family family	d.229.1.1 — MesJ substrate recognition domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	2e21A01
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	2e21A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	59 — Chorismate Mutase Domain, subunit A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2e21B01
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	2e21B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	59 — Chorismate Mutase Domain, subunit A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2e21C01
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	2e21C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	59 — Chorismate Mutase Domain, subunit A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2e21D01
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	2e21D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	59 — Chorismate Mutase Domain, subunit A
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	94.456 Å
Unit-cell length b length_b	82.231 Å
Unit-cell length c length_c	109.431 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	49.010 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2940

Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.

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

tRNA(Ile)-lysidine synthase

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

2e21__assembly_2__model_1

2e21__assembly_2__model_1 | I(q)

2e21__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.

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

tRNA(Ile)-lysidine synthase

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

2e21__assembly_2__model_1

2e21__assembly_2__model_1 | I(q)

2e21__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)