SAXSdb — 1ogf

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

HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	GLYCEROL × 10 CHLORIDE ION × 4 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBSD_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 1–131 Author chain B； PDBConstruct 1–131； UniProt 1–131 Author chain C； PDBConstruct 1–131； UniProt 1–131 Author chain D； PDBConstruct 1–131； UniProt 1–131 Author chain E； PDBConstruct 1–131； UniProt 1–131

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	1ogf
Deposition date deposition_date	2003-04-30
Structure title title	The Structure of Bacillus subtilis RbsD complexed with glycerol
Keywords keywords	RIBOSE, TRANSPORT, SUGAR TRANSPORT; TRANSPORT
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.

1ogf__assembly_1__model_1

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

Download this curve (.dat)

1ogf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ogf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.53 Å
Rg (electron density)	33.29 Å
Total Rg	33.87 Å
Atom count	10084
Residues	1310
Excluded volume	182650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ogf__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
Molecular weight formula_weight	14244.4 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	5411

MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	369

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1ogfa_
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.133.1.1 — RbsD-like

Domain ID domain_id	d1ogfb_
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.133.1.1 — RbsD-like

Domain ID domain_id	d1ogfc_
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.133.1.1 — RbsD-like

Domain ID domain_id	d1ogfd_
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.133.1.1 — RbsD-like

Domain ID domain_id	d1ogfe_
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.133.1.1 — RbsD-like

CATH v4.4 (5 domains)

Domain ID domain_id	1ogfA01
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	1ogfB01
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	1ogfC01
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	1ogfD01
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	1ogfE01
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	122.314 Å
Unit-cell length b length_b	106.222 Å
Unit-cell length c length_c	82.648 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2500

The Structure of Bacillus subtilis RbsD complexed with glycerol

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

HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD

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

1ogf__assembly_1__model_1

1ogf__assembly_1__model_1 | I(q)

1ogf__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

The Structure of Bacillus subtilis RbsD complexed with glycerol

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

HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD

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

1ogf__assembly_1__model_1

1ogf__assembly_1__model_1 | I(q)

1ogf__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)