SAXSdb — 2ixl

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

DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

STREPTOCOCCUS SUIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE × 2 NICKEL (II) ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE × 2 NICKEL (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8GIQ0_STRSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 1–197 Author chain B； PDBConstruct 1–197； UniProt 1–197 Author chain C； PDBConstruct 1–197； UniProt 1–197 Author chain D； PDBConstruct 1–197； UniProt 1–197

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	2ixl
Deposition date deposition_date	2006-07-08
Structure title title	RmlC S. suis with dTDP-rhamnose
Keywords keywords	EPIMERISE, EPIMERASE, ISOMERASE, EPIMERIZE; ISOMERASE
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.

2ixl__assembly_1__model_1

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

Download this curve (.dat)

2ixl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ixl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.67 Å
Rg (electron density)	21.65 Å
Total Rg	22.66 Å
Atom count	3232
Residues	391
Excluded volume	57313 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ixl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ixl__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	DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
Molecular weight formula_weight	22488.3 kDa
EC 编号 ec_number	5.1.3.13
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	7954

MTENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL

Source Source

Source organism organism	STREPTOCOCCUS SUIS
NCBI taxonomy ID ncbi_taxonomy_id	1307
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
Molecular weight formula_weight	548.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1475

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ixla_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.1 — dTDP-sugar isomerase

Domain ID domain_id	d2ixlb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.1 — dTDP-sugar isomerase

Domain ID domain_id	d2ixlc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.1 — dTDP-sugar isomerase

Domain ID domain_id	d2ixld_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.1 — dTDP-sugar isomerase

CATH v4.4 (4 domains)

Domain ID domain_id	2ixlA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2ixlB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2ixlC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2ixlD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	51.408 Å
Unit-cell length b length_b	141.526 Å
Unit-cell length c length_c	53.586 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.57 °
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	1.600 Å
Low-resolution limit resolution_low	42.680 Å
R factor r_factor	0.1690
R_work r_work	0.1670
R_free r_free	0.2120

RmlC S. suis with dTDP-rhamnose

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

DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

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

2ixl__assembly_1__model_1

2ixl__assembly_1__model_1 | I(q)

2ixl__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

RmlC S. suis with dTDP-rhamnose

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

DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

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

2ixl__assembly_1__model_1

2ixl__assembly_1__model_1 | I(q)

2ixl__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)