SAXSdb — 2i1o

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

Nicotinate Phosphoribosyltransferase

Thermoplasma acidophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 36 ZINC ION × 12 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 12 ACETIC ACID × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9HJ28_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–398； UniProt 1–392

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	2i1o
Deposition date deposition_date	2006-08-14
Structure title title	Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum
Keywords keywords	;Nicotinate Phosphoribosyltransferase, zin ion, zinc finger motif, Structural Genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, TRANSFERASE ;; TRANSFERASE
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.

2i1o__assembly_1__model_1

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

Download this curve (.dat)

2i1o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2i1o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.11 Å
Rg (electron density)	42.41 Å
Total Rg	42.83 Å
Atom count	18450
Residues	2334
Excluded volume	329090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2i1o__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	Nicotinate Phosphoribosyltransferase
Molecular weight formula_weight	43695.1 kDa
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	3196

GGGGGGMNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFKDIS

Source Source

Source organism organism	Thermoplasma acidophilum
NCBI taxonomy ID ncbi_taxonomy_id	2303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2i1oa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
Family Family family	d.41.2.1 — NadC N-terminal domain-like

Domain ID domain_id	d2i1oa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
Family Family family	c.1.17.1 — NadC C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	2i1oA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	20 — Quinolinate phosphoribosyl transferase, N-terminal domain

Domain ID domain_id	2i1oA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	135.012 Å
Unit-cell length b length_b	135.012 Å
Unit-cell length c length_c	120.324 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2500

Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum

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

Nicotinate Phosphoribosyltransferase

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

2i1o__assembly_1__model_1

2i1o__assembly_1__model_1 | I(q)

2i1o__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum

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

Nicotinate Phosphoribosyltransferase

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

2i1o__assembly_1__model_1

2i1o__assembly_1__model_1 | I(q)

2i1o__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)