SAXSdb — 1upg

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

TRANSCRIPTIONAL REPRESSOR TRAM

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	TRAM_AGRTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 1–102 Author chain B； PDBConstruct 1–102； UniProt 1–102

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	1upg
Deposition date deposition_date	2003-09-30
Structure title title	Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens
Keywords keywords	TRANSCRIPTION REPRESSOR, NEGATIVE REGULATOR, QUORUM-SENSING, CONJUGATION, TRANSCRIPTION REGULATION, REPRESSOR; TRANSCRIPTION REPRESSOR
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.

1upg__assembly_1__model_1

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

Download this curve (.dat)

1upg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1upg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.88 Å
Rg (electron density)	18.06 Å
Total Rg	18.81 Å
Atom count	1483
Residues	186
Excluded volume	26775 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1upg__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

SCOP 2.08 (2 domains)

Domain ID domain_id	d1upga_
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.13 — Transcriptional repressor TraM
Family Family family	a.2.13.1 — Transcriptional repressor TraM

Domain ID domain_id	d1upgb_
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.13 — Transcriptional repressor TraM
Family Family family	a.2.13.1 — Transcriptional repressor TraM

CATH v4.4 (2 domains)

Domain ID domain_id	1upgA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

Domain ID domain_id	1upgB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

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Unit-cell length a length_a	76.436 Å
Unit-cell length b length_b	47.097 Å
Unit-cell length c length_c	47.469 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	1.800 Å
Low-resolution limit resolution_low	47.670 Å
R factor r_factor	0.1880
R_work r_work	0.1860
R_free r_free	0.2160

Description description	TRANSCRIPTIONAL REPRESSOR TRAM
Molecular weight formula_weight	11555.9 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	1619

Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens

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

TRANSCRIPTIONAL REPRESSOR TRAM

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

1upg__assembly_1__model_1

1upg__assembly_1__model_1 | I(q)

1upg__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	AGROBACTERIUM TUMEFACIENS
NCBI taxonomy ID ncbi_taxonomy_id	358
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	129

Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens

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

TRANSCRIPTIONAL REPRESSOR TRAM

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

1upg__assembly_1__model_1

1upg__assembly_1__model_1 | I(q)

1upg__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)