SAXSdb — 2q1u

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

Putative nucleotide sugar epimerase/ dehydratase

Bordetella bronchiseptica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 URIDINE-5'-DIPHOSPHATE × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87989_BORBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–377； UniProt 1–357 Author chain B； PDBConstruct 21–377； UniProt 1–357

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	2q1u
Deposition date deposition_date	2007-05-25
Structure title title	Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP
Keywords keywords	ROSSMANN FOLD, PROTEIN-NAD+ COMPLEX, PROTEIN-UDP COMPLEX, Sugar Binding Protein; SUGAR BINDING PROTEIN
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.

2q1u__assembly_1__model_1

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

Download this curve (.dat)

2q1u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2q1u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.11 Å
Rg (electron density)	27.59 Å
Total Rg	28.35 Å
Atom count	5233
Residues	671
Excluded volume	92232 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q1u__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	Putative nucleotide sugar epimerase/ dehydratase
Molecular weight formula_weight	41594.8 kDa
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	5791

MGSSHHHHHHSSGLVPRGSHMPVIMNASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAGCSIAEKTFDDAKATEETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATYGK

Source Source

Source organism organism	Bordetella bronchiseptica
NCBI taxonomy ID ncbi_taxonomy_id	518
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	495

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q1ua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2q1ub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2q1uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2q1uA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

Domain ID domain_id	2q1uB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2q1uB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

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Unit-cell length a length_a	121.851 Å
Unit-cell length b length_b	79.682 Å
Unit-cell length c length_c	84.953 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1774
R_work r_work	0.1770
R_free r_free	0.2110

Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP

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

Putative nucleotide sugar epimerase/ dehydratase

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

2q1u__assembly_1__model_1

2q1u__assembly_1__model_1 | I(q)

2q1u__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP

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

Putative nucleotide sugar epimerase/ dehydratase

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

2q1u__assembly_1__model_1

2q1u__assembly_1__model_1 | I(q)

2q1u__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)