SAXSdb — 2qgi

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

ATP synthase subunits region ORF 6

Rhodobacter blasticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 URIDINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 URIDINE-5'-DIPHOSPHATE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YAT6_RHOBL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–248； UniProt 2–249 Author chain B； PDBConstruct 1–248； UniProt 2–249

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	2qgi
Deposition date deposition_date	2007-06-29
Structure title title	The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus
Keywords keywords	MAJASTRIDIN, ATPASE OPERON, GLYCOSYL TRANSFERASE, ROSSMANN FOLD, UDP-COMPLEX, 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.

2qgi__assembly_2__model_1

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

Download this curve (.dat)

2qgi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qgi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	34.34 Å
Rg (electron density)	33.90 Å
Total Rg	34.36 Å
Atom count	8134
Residues	992
Excluded volume	142790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qgi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qgi__assembly_2__model_1`	tetrameric （4）	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	ATP synthase subunits region ORF 6
Molecular weight formula_weight	28720.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4788

KPVPTYVQDKDESTLMFSVCSLVRDQAKYDRLLESFERFGFTPDKAEFLAADNREGNQFHGFSWHKQMLPRCKGRYVIFCHEDVELVDRGYDDLVAAIEALEEADPKWLVAGVAGSPWRPLNHSVTAQALHISDVFGNDRRRGNVPCRVESLDECFLLMRRLKPVLNSYDMQGFHYYGADLCLQAEFLGGRAYAIDFHLHHYGRAIADENFHRLRQEMAQKYRRWFPGRILHCVTGRVALGGGWYEAR

Source Source

Source organism organism	Rhodobacter blasticus
NCBI taxonomy ID ncbi_taxonomy_id	1075
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	721

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2qgiA01
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	2qgiB01
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	123.370 Å
Unit-cell length b length_b	89.928 Å
Unit-cell length c length_c	69.572 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	12.990 Å
R factor r_factor	0.1600
R_work r_work	0.1590
R_free r_free	0.1840

The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus

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

ATP synthase subunits region ORF 6

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

2qgi__assembly_2__model_1

2qgi__assembly_2__model_1 | I(q)

2qgi__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus

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

ATP synthase subunits region ORF 6

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

2qgi__assembly_2__model_1

2qgi__assembly_2__model_1 | I(q)

2qgi__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)