SAXSdb — 2g5i

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

Glutamyl-tRNA(Gln) amidotransferase subunit A

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B × 1 （P64201） Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C × 1 （P68807） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GATA_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–485； UniProt 1–485

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Staphylococcus aureus

UniProt P64201

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Glutamyl-tRNA(Gln) amidotransferase subunit A × 1 （P63488） Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C × 1 （P68807） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GATB_STAAM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–475； UniProt 1–475

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

Staphylococcus aureus

UniProt P68807

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Glutamyl-tRNA(Gln) amidotransferase subunit A × 1 （P63488） Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B × 1 （P64201） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GATC_STAAM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–100； UniProt 1–100

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	2g5i
Deposition date deposition_date	2006-02-23
Structure title title	Structure of tRNA-Dependent Amidotransferase GatCAB complexed with ADP-AlF4
Keywords keywords	MULTI PROTEIN COMPLEX, LIGASE; 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.

2g5i__assembly_1__model_1

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

Download this curve (.dat)

2g5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2g5i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.27 Å
Rg (electron density)	33.01 Å
Total Rg	33.56 Å
Atom count	7784
Residues	993
Excluded volume	138370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2g5i__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	Glutamyl-tRNA(Gln) amidotransferase subunit A
Molecular weight formula_weight	52858.7 kDa
EC 编号 ec_number	6.3.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7874

MSIRYESVENLLTLIKDKKIKPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELDELQAKDQMDGKLFGIPMGIKDNIITNGLETTCASKMLEGFVPIYESTVMEKLHKENAVLIGKLNMDEFAMGGSTETSYFKKTVNPFDHKAVPGGSSGGSAAAVAAGLVPLSLGSDTGGSIRQPAAYCGVVGMKPTYGRVSRFGLVAFASSLDQIGPLTRNVKDNAIVLEAISGADVNDSTSAPVDDVDFTSEIGKDIKGLKVALPKEYLGEGVADDVKEAVQNAVETLKSLGAVVEEVSLPNTKFGIPSYYVIASSEASSNLSRFDGIRYGYHSKEAHSLEELYKMSRSEGFGKEVKRRIFLGTFALSSGYYDAYYKKSQKVRTLIKNDFDKVFENYDVVVGPTAPTTAFNLGEEIDDPLTMYANDLLTTPVNLAGLPGISVPCGQSNGRPIGLQFIGKPFDEKTLYRVAYQYETQYNLHDVYEKL

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
Molecular weight formula_weight	54794.6 kDa
EC 编号 ec_number	6.3.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLHMEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLNGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELDKRLEHHHHHH

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
Molecular weight formula_weight	11279.5 kDa
EC 编号 ec_number	6.3.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTKVTREEVEHIANLARLQISPEETEEMANTLESILDFAKQNDSADTEGVEPTYHVLDLQNVLREDKAIKGIPQELALKNAKETEDGQFKVPTIMNEEDA

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2g5ia1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.117 — Amidase signature (AS) enzymes
Superfamily Superfamily superfamily	c.117.1 — Amidase signature (AS) enzymes
Family Family family	c.117.1.1 — Amidase signature (AS) enzymes

Domain ID domain_id	d2g5ib1
Class class	a — All alpha proteins
Fold Fold fold	a.182 — GatB/YqeY motif
Superfamily Superfamily superfamily	a.182.1 — GatB/YqeY motif
Family Family family	a.182.1.2 — GatB/GatE C-terminal domain-like

Domain ID domain_id	d2g5ib2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.5 — GatB/GatE catalytic domain-like

Domain ID domain_id	d2g5ic1
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.12 — Glu-tRNAGln amidotransferase C subunit
Family Family family	a.137.12.1 — Glu-tRNAGln amidotransferase C subunit

CATH v4.4 (2 domains)

Domain ID domain_id	2g5iA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1300 — Amidase signature (AS) enzymes
Homologous superfamily homologous superfamily	10 — Amidase signature (AS) domain

Domain ID domain_id	2g5iC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	60 — Glu-tRNAGln amidotransferase C subunit, N-terminal domain

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Unit-cell length a length_a	76.860 Å
Unit-cell length b length_b	85.279 Å
Unit-cell length c length_c	183.625 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.350 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2330
R_free r_free	0.2970

Structure of tRNA-Dependent Amidotransferase GatCAB complexed with ADP-AlF4

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

Glutamyl-tRNA(Gln) amidotransferase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

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

2g5i__assembly_1__model_1

2g5i__assembly_1__model_1 | I(q)

2g5i__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of tRNA-Dependent Amidotransferase GatCAB complexed with ADP-AlF4

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

Glutamyl-tRNA(Gln) amidotransferase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

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

2g5i__assembly_1__model_1

2g5i__assembly_1__model_1 | I(q)

2g5i__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)