SAXSdb — 2xci

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

3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE

AQUIFEX AEOLICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	TETRAETHYLENE GLYCOL × 2 GLYCEROL × 5 NICKEL (II) ION × 2 CHLORIDE ION × 4 BETA-MERCAPTOETHANOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	TETRAETHYLENE GLYCOL × 2 GLYCEROL × 3 NICKEL (II) ION × 2 CHLORIDE ION × 4 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	TETRAETHYLENE GLYCOL × 2 GLYCEROL × 3 NICKEL (II) ION × 1 CHLORIDE ION × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 NICKEL (II) ION × 1 CHLORIDE ION × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLYCEROL × 2 NICKEL (II) ION × 1 CHLORIDE ION × 1 BETA-MERCAPTOETHANOL × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	TETRAETHYLENE GLYCOL × 2 GLYCEROL × 2 NICKEL (II) ION × 1 CHLORIDE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O66663_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–374； UniProt 1–353 Author chain B； PDBConstruct 22–374； UniProt 1–353 Author chain C； PDBConstruct 22–374； UniProt 1–353 Author chain D； PDBConstruct 22–374； UniProt 1–353

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	2xci
Deposition date deposition_date	2010-04-26
Structure title title	Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form
Keywords keywords	TRANSFERASE, KDTA, GSEA, GLYCOSYLTRANSFERASE SUPERFAMILY B, GT-B; 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.

2xci__assembly_1__model_1

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

Download this curve (.dat)

2xci__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xci__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.49 Å
Rg (electron density)	28.49 Å
Total Rg	29.47 Å
Atom count	5828
Residues	707
Excluded volume	106680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xci__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xci__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xci__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2xci__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2xci__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2xci__assembly_6__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 (7)

Entity 1 Entity 1 polymer

Description description	3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
Molecular weight formula_weight	43278.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11857

MGHHHHHHHHHHSSGHIEGRHMQFEVLKRFFPKESLKNCKGALWVHTASIGEFNTFLPILKELKREHRILLTYFSPRAREYLKTKSDFYDCLHPLPLDNPFSVKRFEELSKPKALIVVEREFWPSLIIFTKVPKILVNAYAKGSLIEKILSKKFDLIIMRTQEDVEKFKTFGAKRVFSCGNLKFICQKGKGIKLKGEFIVAGSIHTGEVEIILKAFKEIKKTYSSLKLILVPRHIENAKIFEKKARDFGFKTSFFENLEGDVILVDRFGILKELYPVGKIAIVGGTFVNIGGHNLLEPTCWGIPVIYGPYTHKVNDLKEFLEKEGAGFEVKNETELVTKLTELLSVKKEIKVEEKSREIKGCYLEKLREFLRGL

Source Source

Source organism organism	AQUIFEX AEOLICUS
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 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	248

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2xciA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11720 — 3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain

Domain ID domain_id	2xciA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	2xciB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11720 — 3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain

Domain ID domain_id	2xciB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	2xciC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11720 — 3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain

Domain ID domain_id	2xciC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	2xciD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11720 — 3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain

Domain ID domain_id	2xciD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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Unit-cell length a length_a	132.500 Å
Unit-cell length b length_b	45.820 Å
Unit-cell length c length_c	144.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.854 Å
R factor r_factor	0.2095
R_work r_work	0.2071
R_free r_free	0.2539

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form

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

3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE

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

2xci__assembly_1__model_1

2xci__assembly_1__model_1 | I(q)

2xci__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form

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

3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE

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

2xci__assembly_1__model_1

2xci__assembly_1__model_1 | I(q)

2xci__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)