SAXSdb — 2y6p

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

3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE

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	CYTIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 4 ISOPROPYL ALCOHOL × 1 BETA-MERCAPTOETHANOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CYTIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 4 ISOPROPYL ALCOHOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDSB_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 1–234 Author chain B； PDBConstruct 1–234； UniProt 1–234 Author chain C； PDBConstruct 1–234； UniProt 1–234

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	2y6p
Deposition date deposition_date	2011-01-25
Structure title title	Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB
Keywords keywords	TRANSFERASE, LIPID A; 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.

2y6p__assembly_2__model_1

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

Download this curve (.dat)

2y6p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y6p__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.84 Å
Rg (electron density)	26.28 Å
Total Rg	27.09 Å
Atom count	3814
Residues	458
Excluded volume	68645 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y6p__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y6p__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 (6)

Entity 1 Entity 1 polymer

Description description	3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
Molecular weight formula_weight	27213.5 kDa
EC 编号 ec_number	2.7.7.38
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5973

MRRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKLKNL

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	CYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	483.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2y6pa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.0 — automated matches

Domain ID domain_id	d2y6pb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.0 — automated matches

Domain ID domain_id	d2y6pc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2y6pA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2y6pB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2y6pC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	156.175 Å
Unit-cell length b length_b	51.175 Å
Unit-cell length c length_c	107.514 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.350 Å
R factor r_factor	0.2137
R_work r_work	0.2113
R_free r_free	0.2579

Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB

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

3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE

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

2y6p__assembly_2__model_1

2y6p__assembly_2__model_1 | I(q)

2y6p__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB

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

3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE

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

2y6p__assembly_2__model_1

2y6p__assembly_2__model_1 | I(q)

2y6p__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)