SAXSdb — 2rbc

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

Sugar kinase

Agrobacterium tumefaciens str.

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8UCH8_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–341； UniProt 1–319

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	2rbc
Deposition date deposition_date	2007-09-18
Structure title title	Crystal structure of a putative ribokinase from Agrobacterium tumefaciens
Keywords keywords	;sugar kinase, ribokinase family, ATP-binding site, structural genomics, Agrobacterium tumefaciens, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSFERASE ;; 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.

2rbc__assembly_1__model_1

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

Download this curve (.dat)

2rbc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rbc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.67 Å
Rg (electron density)	29.09 Å
Total Rg	29.62 Å
Atom count	4693
Residues	594
Excluded volume	83538 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rbc__assembly_1__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	Sugar kinase
Molecular weight formula_weight	37365.7 kDa
EC 编号 ec_number	2.7.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2838

MGSSHHHHHHSSGRENLYFQGHMVKEPGGKHVLCVGAAVLDTLFRVADMPKGEGKVLPYEVLQIAEGMASSAAYAVHRMGGRASLWGAVGDDETGTRILRDLSESGIDTSGMTVAPGARSALSTIIIDNRGERLIVPFYDHRLHEKKRACTPEDIALFDAVLVDVRWPELALDVLTVARALGKPAILDGDVAPVETLEGLAPAATHIVFSEPAATRLTGLETVKDMLPVLHARYPQTFIAVTAGPAGCWWTEADDPTVHFQTTMQVEAVDTLAAGDIFHGTFALAMAEGMQSRAAVRLSSVAAALKCTVFGGRIGAPTREETEEAMRQWLERESEPALRASGS

Source Source

Source organism organism	Agrobacterium tumefaciens str.
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	400

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2rbca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2rbcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

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Unit-cell length a length_a	81.024 Å
Unit-cell length b length_b	81.024 Å
Unit-cell length c length_c	139.799 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	32.170 Å
R factor r_factor	0.1900
R_work r_work	0.1880
R_free r_free	0.2280

Crystal structure of a putative ribokinase from Agrobacterium tumefaciens

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

Sugar kinase

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

2rbc__assembly_1__model_1

2rbc__assembly_1__model_1 | I(q)

2rbc__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a putative ribokinase from Agrobacterium tumefaciens

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

Sugar kinase

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

2rbc__assembly_1__model_1

2rbc__assembly_1__model_1 | I(q)

2rbc__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)