SAXSdb — 2q16

▼

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

HAM1 protein homolog

Escherichia coli

UniProt P52061

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 SODIUM ION × 5 SULFATE ION × 1 ;INOSINE 5'-TRIPHOSPHATE ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HAM1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–217； UniProt 1–197 Author chain B； PDBConstruct 21–217； UniProt 1–197

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	2q16
Deposition date deposition_date	2007-05-23
Structure title title	Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP
Keywords keywords	ITP pyrophosphatase x-ray structure enzyme mechanism substrate, HYDROLASE; HYDROLASE
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.

2q16__assembly_1__model_1

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

Download this curve (.dat)

2q16__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2q16__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.76 Å
Rg (electron density)	22.86 Å
Total Rg	23.66 Å
Atom count	2996
Residues	387
Excluded volume	53156 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q16__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	HAM1 protein homolog
Molecular weight formula_weight	23476.0 kDa
EC 编号 ec_number	3.6.1.19
Mutation mutation	D69A
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	3419

MGSSHHHHHHSSGLVPRGSHMQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADASGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRNGGS

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;INOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	508.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	410

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q16a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.0 — automated matches

Domain ID domain_id	d2q16b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2q16A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2q16B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	120.646 Å
Unit-cell length b length_b	120.646 Å
Unit-cell length c length_c	66.562 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	26.980 Å
R factor r_factor	0.1728
R_work r_work	0.1709
R_free r_free	0.2083

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP

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

HAM1 protein homolog

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

2q16__assembly_1__model_1

2q16__assembly_1__model_1 | I(q)

2q16__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP

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

HAM1 protein homolog

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

2q16__assembly_1__model_1

2q16__assembly_1__model_1 | I(q)

2q16__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)