SAXSdb — 1wx1

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

nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Thermus thermophilus HB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COBT_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 1–335 Author chain B； PDBConstruct 1–335； UniProt 1–335

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	1wx1
Deposition date deposition_date	2005-01-19
Structure title title	Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8
Keywords keywords	structural genomics, Thermus thermophilus HB8, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

1wx1__assembly_1__model_1

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

Download this curve (.dat)

1wx1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wx1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.46 Å
Rg (electron density)	26.46 Å
Total Rg	27.20 Å
Atom count	4821
Residues	660
Excluded volume	86310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wx1__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 (3)

Entity 1 Entity 1 polymer

Description description	nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Molecular weight formula_weight	34788.3 kDa
EC 编号 ec_number	2.4.2.21
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	5270

MDPEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVGRGTGVGEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	449

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wx1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.39 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Superfamily Superfamily superfamily	c.39.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Family Family family	c.39.1.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

Domain ID domain_id	d1wx1b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.39 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Superfamily Superfamily superfamily	c.39.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Family Family family	c.39.1.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

CATH v4.4 (4 domains)

Domain ID domain_id	1wx1A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1610 — 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1
Homologous superfamily homologous superfamily	10 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain

Domain ID domain_id	1wx1A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10210 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain

Domain ID domain_id	1wx1B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1610 — 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1
Homologous superfamily homologous superfamily	10 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain

Domain ID domain_id	1wx1B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10210 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain

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Unit-cell length a length_a	107.357 Å
Unit-cell length b length_b	107.357 Å
Unit-cell length c length_c	244.665 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	32

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	29.680 Å
R factor r_factor	0.1870
R_work r_work	0.1850
R_free r_free	0.2190

Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8

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

nicotinate-nucleotide--dimethylbenzimidazole 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

1wx1__assembly_1__model_1

1wx1__assembly_1__model_1 | I(q)

1wx1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8

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

nicotinate-nucleotide--dimethylbenzimidazole 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

1wx1__assembly_1__model_1

1wx1__assembly_1__model_1 | I(q)

1wx1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)