2odf

The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION

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

Hypothetical protein Atu2144

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 × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8UDI1_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 1–257 Author chain B； PDBConstruct 1–257； UniProt 1–257 Author chain C； PDBConstruct 1–257； UniProt 1–257 Author chain D； PDBConstruct 1–257； UniProt 1–257 Author chain E； PDBConstruct 1–257； UniProt 1–257 Author chain F； PDBConstruct 1–257； UniProt 1–257 Author chain G； PDBConstruct 1–257； UniProt 1–257 Author chain H； PDBConstruct 1–257； UniProt 1–257

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	2odf
Deposition date deposition_date	2006-12-22
Structure title title	The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens
Keywords keywords	;Structural genomics, Agrobacterium tumefaciens, unknown function, PSI-2, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics ;; 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.

2odf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2odf__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2odf__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	26.38 Å
Rg (electron density)	25.74 Å
Total Rg	26.52 Å
Atom count	3851
Residues	500
Excluded volume	68001 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2odf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2odf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2odf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2odf__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein Atu2144
Molecular weight formula_weight	28099.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	17054

MTVRSRFFTEAEGKAVGVENAAAKGDVLLVCEHASATIPQKYGTLGLSADVLSSHAAWDPGALAVARLLSEKFHATLVYQRFSRLVYDCNRPPESPSAMPVKSEIYDIPGNFDLDEAERFARTSALYVPFHDRVSEIIAERQAAGRKVVVVTIHSFTPVYHGRFREVEIGILHDNDSRLADAMLAGAEGASLTVRRNDPYGPEDGVTHTLRLHALPDGLLNVMIEIRNDLIANEGEQAAIAGFLHELMGKALSSIEE

Source Source

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

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	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1613

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2odfa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odff_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

Domain ID domain_id	d2odfh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.9 — FGase-like

CATH v4.4 (8 domains)

Domain ID domain_id	2odfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	2odfH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

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Unit-cell length a length_a	110.523 Å
Unit-cell length b length_b	89.765 Å
Unit-cell length c length_c	120.365 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	120.000 Å
R factor r_factor	0.1911
R_work r_work	0.1889
R_free r_free	0.2339

The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens

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

Hypothetical protein Atu2144

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

2odf__assembly_3__model_1

2odf__assembly_3__model_1 | I(q)

2odf__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens

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

Hypothetical protein Atu2144

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

2odf__assembly_3__model_1

2odf__assembly_3__model_1 | I(q)

2odf__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)