SAXSdb — 3o98

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

Bifunctional glutathionylspermidine synthetase/amidase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLUTATHIONYLSPERMIDINE × 1 ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GSP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–619； UniProt 1–619 Author chain B； PDBConstruct 1–619； UniProt 1–619

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	3o98
Deposition date deposition_date	2010-08-04
Structure title title	Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp
Keywords keywords	Ligase, Hydrolase; Ligase, Hydrolase
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.

3o98__assembly_1__model_1

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

Download this curve (.dat)

3o98__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3o98__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.77 Å
Rg (electron density)	33.80 Å
Total Rg	34.36 Å
Atom count	9762
Residues	1202
Excluded volume	172990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3o98__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 (5)

Entity 1 Entity 1 polymer

Description description	Bifunctional glutathionylspermidine synthetase/amidase
Molecular weight formula_weight	70579.7 kDa
EC 编号 ec_number	6.3.1.8, 3.5.1.78
Mutation mutation	C59A
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	9968

MSKGTTSQDAPFGTLLGYAPGGVAIYSSDYSSLDPQEYEDDAVFRSYIDDEYMGHKWQAVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREVSDREFAAVPIRTGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVVKK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLUTATHIONYLSPERMIDINE
Molecular weight formula_weight	434.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3o98A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
Homologous superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

Domain ID domain_id	3o98B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
Homologous superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

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Unit-cell length a length_a	60.380 Å
Unit-cell length b length_b	76.200 Å
Unit-cell length c length_c	84.220 Å
Unit-cell angle α angle_alpha	70.81 °
Unit-cell angle β angle_beta	74.37 °
Unit-cell angle γ angle_gamma	78.64 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2197
R_free r_free	0.2624

Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp

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

Bifunctional glutathionylspermidine synthetase/amidase

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

3o98__assembly_1__model_1

3o98__assembly_1__model_1 | I(q)

3o98__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp

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

Bifunctional glutathionylspermidine synthetase/amidase

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

3o98__assembly_1__model_1

3o98__assembly_1__model_1 | I(q)

3o98__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)