SAXSdb — 3dnh

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

uncharacterized protein Atu2129

Agrobacterium tumefaciens

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CI98_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–256； UniProt 1–254 Author chain B； PDBConstruct 3–256； UniProt 1–254

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	3dnh
Deposition date deposition_date	2008-07-02
Structure title title	The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58
Keywords keywords	;APC6114, protein Atu2129, Agrobacterium tumefaciens str. C58, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG, unknown function ;; structural genomics, unknown function
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.

3dnh__assembly_1__model_1

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

Download this curve (.dat)

3dnh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dnh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.46 Å
Rg (electron density)	23.67 Å
Total Rg	24.63 Å
Atom count	3541
Residues	463
Excluded volume	63353 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dnh__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3dnhA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	3dnhA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	180 — Split barrel-like
Homologous superfamily homologous superfamily	10 — PNP-oxidase-like

Domain ID domain_id	3dnhB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	3dnhB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	180 — Split barrel-like
Homologous superfamily homologous superfamily	10 — PNP-oxidase-like

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Unit-cell length a length_a	53.651 Å
Unit-cell length b length_b	66.830 Å
Unit-cell length c length_c	69.967 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.19 °
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	1.940 Å
Low-resolution limit resolution_low	29.760 Å
R factor r_factor	0.1893
R_work r_work	0.1867
R_free r_free	0.2380

Description description	uncharacterized protein Atu2129
Molecular weight formula_weight	27730.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3843

The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58

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

uncharacterized protein Atu2129

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

3dnh__assembly_1__model_1

3dnh__assembly_1__model_1 | I(q)

3dnh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	289

The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58

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

uncharacterized protein Atu2129

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

3dnh__assembly_1__model_1

3dnh__assembly_1__model_1 | I(q)

3dnh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)