2im5

Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis

Method: X-RAY DIFFRACTION

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

Nicotinate phosphoribosyltransferase

Porphyromonas gingivalis

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
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	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	Q7MXV0_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394 Author chain C； PDBConstruct 1–394； UniProt 1–394 Author chain D； PDBConstruct 1–394； UniProt 1–394

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	2im5
Deposition date deposition_date	2006-10-03
Structure title title	Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis
Keywords keywords	;Structural genomics, NYSGXRC, phosphoribosyltransferase, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, 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.

2im5__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2im5__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2im5__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.76 Å
Rg (electron density)	20.50 Å
Total Rg	21.49 Å
Atom count	3171
Residues	389
Excluded volume	56539 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2im5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2im5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2im5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2im5__assembly_4__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2im5a1
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.41.2.2 — Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like

Domain ID domain_id	d2im5a2
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.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

Domain ID domain_id	d2im5b1
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.41.2.2 — Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like

Domain ID domain_id	d2im5b2
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.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

Domain ID domain_id	d2im5c1
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.41.2.2 — Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like

Domain ID domain_id	d2im5c2
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.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

Domain ID domain_id	d2im5d1
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.41.2.2 — Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like

Domain ID domain_id	d2im5d2
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.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	2im5A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	140 — nicotinate phosphoribosyltransferase
Homologous superfamily homologous superfamily	10 — nicotinate phosphoribosyltransferase

Domain ID domain_id	2im5B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	140 — nicotinate phosphoribosyltransferase
Homologous superfamily homologous superfamily	10 — nicotinate phosphoribosyltransferase

Domain ID domain_id	2im5C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	140 — nicotinate phosphoribosyltransferase
Homologous superfamily homologous superfamily	10 — nicotinate phosphoribosyltransferase

Domain ID domain_id	2im5D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	140 — nicotinate phosphoribosyltransferase
Homologous superfamily homologous superfamily	10 — nicotinate phosphoribosyltransferase

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Unit-cell length a length_a	88.873 Å
Unit-cell length b length_b	101.131 Å
Unit-cell length c length_c	191.051 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	24.750 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2410

Description description	Nicotinate phosphoribosyltransferase
Molecular weight formula_weight	45532.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13047

Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis

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

2im5__assembly_4__model_1

2im5__assembly_4__model_1 | I(q)

2im5__assembly_4__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	837
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	363

Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis

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

2im5__assembly_4__model_1

2im5__assembly_4__model_1 | I(q)

2im5__assembly_4__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)