SAXSdb — 1j5y

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

TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NICKEL (II) ION × 1 POTASSIUM ION × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	NICKEL (II) ION × 4 POTASSIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1T8_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–187； UniProt 1–175

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	1j5y
Deposition date deposition_date	2002-07-05
Structure title title	Crystal structure of transcriptional regulator (TM1602) from Thermotoga maritima at 2.3 A resolution
Keywords keywords	;STRUCTURAL GENOMICS, TM1602, TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY, JCSG, CONSERVED HYPOTHETICAL PROTEIN, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, TRANSCRIPTION ;; TRANSCRIPTION
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.

1j5y__assembly_1__model_1

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

Download this curve (.dat)

1j5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.58 Å
Rg (electron density)	18.98 Å
Total Rg	19.86 Å
Atom count	1349
Residues	167
Excluded volume	24478 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j5y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1j5y__assembly_2__model_1`	tetrameric （4）	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	TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
Molecular weight formula_weight	21373.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1446

MGSDKIHHHHHHMHMKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGGKSGVSRLVAVKHAPEEIKEELLCVVRNGGRIVDVIVEHPVYGEIRGIIDVSSEEEVLKFVNLMEMAKTEPLLTLSGGVHLHTIEAPDEETMERIMRELKKKGFLIEEG

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1j5ya1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.1 — Biotin repressor-like

Domain ID domain_id	d1j5ya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.94 — HPr-like
Superfamily Superfamily superfamily	d.94.2 — Putative transcriptional regulator TM1602, C-terminal domain
Family Family family	d.94.2.1 — Putative transcriptional regulator TM1602, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1j5yA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1j5yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1340 — Histidine-containing Protein; Chain: A;
Homologous superfamily homologous superfamily	20 — 3H domain

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Unit-cell length a length_a	90.957 Å
Unit-cell length b length_b	90.957 Å
Unit-cell length c length_c	90.957 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	12

Space group space_group	P 2 3
Space-group number int_tables_number	195
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2340

Crystal structure of transcriptional regulator (TM1602) from Thermotoga maritima at 2.3 A resolution

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

TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY

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

1j5y__assembly_1__model_1

1j5y__assembly_1__model_1 | I(q)

1j5y__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 transcriptional regulator (TM1602) from Thermotoga maritima at 2.3 A resolution

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

TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY

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

1j5y__assembly_1__model_1

1j5y__assembly_1__model_1 | I(q)

1j5y__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)