SAXSdb — 3siw

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

Nodulation fucosyltransferase NodZ

Bradyrhizobium sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHATE ION × 3 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9AQ17_BRASW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–324； UniProt 1–324

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	3siw
Deposition date deposition_date	2011-06-20
Structure title title	Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP
Keywords keywords	;family GT23 glycosyltransferase, GT-B fold, alfa1, 6-fucosyltransferase, nodulation protein, chitooligosaccharide fucosylation, Nod Factor biosynthesis, nitrogen fixation, legume-rhizobium symbiosis, 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.

3siw__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3siw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3siw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.08 Å
Rg (electron density)	29.68 Å
Total Rg	30.30 Å
Atom count	4752
Residues	580
Excluded volume	83822 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3siw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3siw__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Nodulation fucosyltransferase NodZ
Molecular weight formula_weight	37829.0 kDa
EC 编号 ec_number	2.4.1.-
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	2680

MTKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRHGNGEDIMEHAPYWADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPKRFQADRAGPLHSAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTMIDNPYEHFAASHHHHHH

Source Source

Source organism organism	Bradyrhizobium sp.
NCBI taxonomy ID ncbi_taxonomy_id	133505
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3siwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11340 —

Domain ID domain_id	3siwA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11350 —

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7. Citations (7)

Structures of NodZ alpha-1,6-fucosyltransferase in complex with GDP and GDP-fucose

Acta Crystallogr.,Sect.D (2012)

PMID: 22281745 · DOI: 10.1107/S0907444911053157 PRIMARY

High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor

Acta Biochim.Pol. (2007)

Structure and Mechanism of Helicobacter pylori Fucosyltransferase: A basis for lipopolysaccharide variation and inhibitor design

J.Biol.Chem. (2007)

Crystal structure of human alpha 1,6-fucosyltransferase, FUT8

Glycobiology (2007)

Cloning, purification, crystallization and preliminary crystallographic studies of bradyrhizobium fucosyltransferase NodZ

Acta Crystallogr.,Sect.D (2004)

;Bacterial nodulation protein NodZ is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin ;

Proc.Natl.Acad.Sci.USA (1997)

Rhizobium sp. strain NGR234 NodZ protein is a fucosyltransferase

J. Bacteriol. (1997)

Unit-cell length a length_a	123.900 Å
Unit-cell length b length_b	123.900 Å
Unit-cell length c length_c	95.200 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	46.730 Å
R factor r_factor	0.1737
R_work r_work	0.1721
R_free r_free	0.2173

Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP

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

Nodulation fucosyltransferase NodZ

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

3siw__assembly_2__model_1

3siw__assembly_2__model_1 | I(q)

3siw__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (7)

Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP

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

Nodulation fucosyltransferase NodZ

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

3siw__assembly_2__model_1

3siw__assembly_2__model_1 | I(q)

3siw__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (7)