3e7n

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

Method: X-RAY DIFFRACTION

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

D-ribose high-affinity transport system

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	1,2-ETHANEDIOL × 10 water × 10	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 10	1,2-ETHANEDIOL × 8 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZKW0_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–142； UniProt 1–139 Author chain B； PDBConstruct 4–142； UniProt 1–139 Author chain C； PDBConstruct 4–142； UniProt 1–139 Author chain D； PDBConstruct 4–142； UniProt 1–139 Author chain E； PDBConstruct 4–142； UniProt 1–139 Author chain F； PDBConstruct 4–142； UniProt 1–139 Author chain G； PDBConstruct 4–142； UniProt 1–139 Author chain H； PDBConstruct 4–142； UniProt 1–139 Author chain I； PDBConstruct 4–142； UniProt 1–139 Author chain J； PDBConstruct 4–142； UniProt 1–139 Author chain K； PDBConstruct 4–142； UniProt 1–139 Author chain L； PDBConstruct 4–142； UniProt 1–139 Author chain M； PDBConstruct 4–142； UniProt 1–139 Author chain N； PDBConstruct 4–142； UniProt 1–139 Author chain O； PDBConstruct 4–142； UniProt 1–139

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	3e7n
Deposition date deposition_date	2008-08-18
Structure title title	Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2
Keywords keywords	;D-ribose transport system, rbsD, CSGID, Structural Genomics, NIAID Structural Genomics Centers for Infectious Diseases, Center for Structural Genomics of Infectious Diseases, TRANSPORT PROTEIN ;; TRANSPORT 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.

3e7n__assembly_1__model_1

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

Download this curve (.dat)

3e7n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e7n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.82 Å
Rg (electron density)	34.04 Å
Total Rg	34.45 Å
Atom count	10736
Residues	1366
Excluded volume	192210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e7n__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e7n__assembly_2__model_1`	decameric （10）	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 (3)

Entity 1 Entity 1 polymer

Description description	D-ribose high-affinity transport system
Molecular weight formula_weight	15664.2 kDa
Source method src_method	man
Copy count entity_count	15

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Atom count atom_count	16381

SNAMKKGTVLNSEISSVISRLGHTDTLVVCDAGLPIPNSTARIDMALTQGVPSFMQVVDVVTREMQVEAAILATEIKQQNPQLHETLLTHLEQLQQHQGNTIKISYTTHEQFKKLTADSQAVIRSGECSPYANVILCAGVTF

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (30 domains)

Domain ID domain_id	d3e7na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7na2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7ne1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7ne2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7ng1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7ng2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7ni1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7ni2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nj1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nj2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nk1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nk2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nl1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nl2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nm1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nm2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7nn1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7nn2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e7no1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.133 — RbsD-like
Superfamily Superfamily superfamily	c.133.1 — RbsD-like
Family Family family	c.133.1.0 — automated matches

Domain ID domain_id	d3e7no2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (15 domains)

Domain ID domain_id	3e7nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

Domain ID domain_id	3e7nO01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1650 — RbsD-like fold
Homologous superfamily homologous superfamily	10 — RbsD-like domain

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Unit-cell length a length_a	293.042 Å
Unit-cell length b length_b	92.726 Å
Unit-cell length c length_c	93.601 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	60

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

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1928
R_work r_work	0.1907
R_free r_free	0.2326

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

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

D-ribose high-affinity transport system

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

3e7n__assembly_1__model_1

3e7n__assembly_1__model_1 | I(q)

3e7n__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (30 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

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

D-ribose high-affinity transport system

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

3e7n__assembly_1__model_1

3e7n__assembly_1__model_1 | I(q)

3e7n__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (30 domains)

CATH v4.4 (15 domains)

7. Citations (1)