3d01

Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION

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

Uncharacterized protein

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 3	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 3 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 4 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CJ63_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–165； UniProt 1–156 Author chain B； PDBConstruct 10–165； UniProt 1–156 Author chain C； PDBConstruct 10–165； UniProt 1–156 Author chain D； PDBConstruct 10–165； UniProt 1–156 Author chain E； PDBConstruct 10–165； UniProt 1–156 Author chain F； PDBConstruct 10–165； UniProt 1–156 Author chain G； PDBConstruct 10–165； UniProt 1–156 Author chain H； PDBConstruct 10–165； UniProt 1–156 Author chain I； PDBConstruct 10–165； UniProt 1–156 Author chain J； PDBConstruct 10–165； UniProt 1–156 Author chain K； PDBConstruct 10–165； UniProt 1–156 Author chain L； PDBConstruct 10–165； UniProt 1–156

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	3d01
Deposition date deposition_date	2008-04-30
Structure title title	Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens
Keywords keywords	;Protein with unknown function, structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, 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.

3d01__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d01__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d01__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	22.57 Å
Rg (electron density)	21.37 Å
Total Rg	22.32 Å
Atom count	3513
Residues	461
Excluded volume	63417 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d01__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d01__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3d01__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3d01__assembly_4__model_1`	trimeric （3）	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	Uncharacterized protein
Molecular weight formula_weight	17397.5 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	15234

GTENLYFQGMSDVIEGRLKELGFTLPVAAAPAANYVPFTISGNLLYVSGQLPMESGKIAVTGLVGRDVDVASAQRAAELCAVNILAQVKAALNGDLSKIRRVIKLNGFVASVPEFVEQHLVINGASNLIATVLGEPGRHARAAVGMASLPFNASVEIDAIVEIDV

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1074

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d3d01a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01f1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01g1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01g2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01h1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01i1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01i2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01j1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01j2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01k1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01k2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d01l1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.0 — automated matches

Domain ID domain_id	d3d01l2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	3d01A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01G00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01I00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01J00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01K00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	3d01L00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

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Unit-cell length a length_a	93.623 Å
Unit-cell length b length_b	93.600 Å
Unit-cell length c length_c	93.628 Å
Unit-cell angle α angle_alpha	68.20 °
Unit-cell angle β angle_beta	67.87 °
Unit-cell angle γ angle_gamma	68.14 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	46.130 Å
R factor r_factor	0.1807
R_work r_work	0.1789
R_free r_free	0.2141

Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens

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

Uncharacterized protein

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

3d01__assembly_4__model_1

3d01__assembly_4__model_1 | I(q)

3d01__assembly_4__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) 36 domains

SCOP 2.08 (24 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens

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

Uncharacterized protein

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

3d01__assembly_4__model_1

3d01__assembly_4__model_1 | I(q)

3d01__assembly_4__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) 36 domains

SCOP 2.08 (24 domains)

CATH v4.4 (12 domains)

7. Citations (1)