SAXSdb — 1vki

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

HYPOTHETICAL PROTEIN ATU3699

Agrobacterium tumefaciens str. C58

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 × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U9M7_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–181； UniProt 1–169 Author chain B； PDBConstruct 13–181； UniProt 1–169

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	1vki
Deposition date deposition_date	2004-05-24
Structure title title	Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, translation; TRANSLATION
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.

1vki__assembly_1__model_1

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

Download this curve (.dat)

1vki__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vki__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.59 Å
Rg (electron density)	20.79 Å
Total Rg	21.57 Å
Atom count	2584
Residues	331
Excluded volume	46094 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	HYPOTHETICAL PROTEIN ATU3699
Molecular weight formula_weight	20051.6 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	3124

MGSDKIHHHHHHMTENSRKTATELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENAVVDLKSVHKTIGAASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAPLVLKVSE

Source Source

Source organism organism	Agrobacterium tumefaciens str. C58
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	510

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vkia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.1 — YbaK/ProRS associated domain

Domain ID domain_id	d1vkib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.1 — YbaK/ProRS associated domain

CATH v4.4 (2 domains)

Domain ID domain_id	1vkiA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

Domain ID domain_id	1vkiB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

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Unit-cell length a length_a	35.997 Å
Unit-cell length b length_b	64.848 Å
Unit-cell length c length_c	77.427 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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	49.340 Å
R factor r_factor	0.1537
R_work r_work	0.1520
R_free r_free	0.1850

Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution

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

HYPOTHETICAL PROTEIN ATU3699

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

1vki__assembly_1__model_1

1vki__assembly_1__model_1 | I(q)

1vki__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution

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

HYPOTHETICAL PROTEIN ATU3699

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

1vki__assembly_1__model_1

1vki__assembly_1__model_1 | I(q)

1vki__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)