SAXSdb — 3pnv

▼

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

Glutamyl-tRNA synthetase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYE_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–505； UniProt 1–490 Author chain B； PDBConstruct 16–505； UniProt 1–490

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	3pnv
Deposition date deposition_date	2010-11-19
Structure title title	V369M mutant of Glutamyl-tRNA synthetase from Mycobacterium tuberculosis
Keywords keywords	non-discriminating glutamyl-trna aminoacylation, ATP-binding, Nucleotide-binding, 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.

3pnv__assembly_1__model_1

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

Download this curve (.dat)

3pnv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pnv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.49 Å
Rg (electron density)	31.71 Å
Total Rg	32.04 Å
Atom count	3745
Residues	481
Excluded volume	66218 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pnv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pnv__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Glutamyl-tRNA synthetase
Molecular weight formula_weight	55635.8 kDa
EC 编号 ec_number	6.1.1.17
Mutation mutation	V369M
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	7687

HHHHHHSSGLVPRGSMTATETVRVRFCPSPTGTPHVGLVRTALFNWAYARHTGGTFVFRIEDTDAQRDSEESYLALLDALRWLGLDWDEGPEVGGPYGPYRQSQRAEIYRDVLARLLAAGEAYHAFSTPEEVEARHVAAGRNPKLGYDNFDRHLTDAQRAAYLAEGRQPVVRLRMPDDDLAWNDLVRGPVTFAAGSVPDFALTRASGDPLYTLVNPCDDALMKITHVLRGEDLLPSTPRQLALHQALIRIGVAERIPKFAHLPTVLGEGTKKLSKRDPQSNLFAHRDRGFIPEGLLNYLALLGWSIADDHDLFGLDEMVAAFDVADVNSSPARFDQKKADALNAEHIRMLDVGDFTVRLRDHLDTHGHHIALDEAAFAAAAELMQTRIVVLGDAWELLKFFNDDQYVIDPKAAAKELGPDGAAVLDAALAALTSVTDWTAPLIEAALKDALIEGLALKPRKAFSPIRVAATGTTVSPPLFESLELLGRDRSMQRLRAARQLVGHA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

▼

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3pnvA01
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	3pnvA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	800 — Glutamyl-tRNA Synthetase; domain 3
Homologous superfamily homologous superfamily	10 — Glutamyl-tRNA Synthetase; Domain 3

Domain ID domain_id	3pnvA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1160 — Glutamyl-tRNA Synthetase; domain 2
Homologous superfamily homologous superfamily	10 — Glutamyl-trna Synthetase; Domain 2

Domain ID domain_id	3pnvA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	70 — Glutamate-tRNA synthetase, class I, anticodon-binding domain 1

Domain ID domain_id	3pnvA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	3pnvB01
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	3pnvB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	800 — Glutamyl-tRNA Synthetase; domain 3
Homologous superfamily homologous superfamily	10 — Glutamyl-tRNA Synthetase; Domain 3

Domain ID domain_id	3pnvB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1160 — Glutamyl-tRNA Synthetase; domain 2
Homologous superfamily homologous superfamily	10 — Glutamyl-trna Synthetase; Domain 2

Domain ID domain_id	3pnvB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	70 — Glutamate-tRNA synthetase, class I, anticodon-binding domain 1

Domain ID domain_id	3pnvB05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	350 —

▶

Unit-cell length a length_a	43.434 Å
Unit-cell length b length_b	210.346 Å
Unit-cell length c length_c	57.979 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	10.410 Å
R factor r_factor	0.2746
R_work r_work	0.2724
R_free r_free	0.3158

V369M mutant of Glutamyl-tRNA synthetase from Mycobacterium tuberculosis

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

Glutamyl-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

3pnv__assembly_1__model_1

3pnv__assembly_1__model_1 | I(q)

3pnv__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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

V369M mutant of Glutamyl-tRNA synthetase from Mycobacterium tuberculosis

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

Glutamyl-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

3pnv__assembly_1__model_1

3pnv__assembly_1__model_1 | I(q)

3pnv__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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)