SAXSdb — 3d8u

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

PurR transcriptional regulator

Vibrio parahaemolyticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87JL7_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–275； UniProt 71–342 Author chain B； PDBConstruct 4–275； UniProt 71–342

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	3d8u
Deposition date deposition_date	2008-05-23
Structure title title	The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633
Keywords keywords	;APC91343.1, PurR, transcriptional regulator, Vibrio parahaemolyticus RIMD 2210633, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG, DNA-binding, Transcription, Transcription regulation, transcription regulator ;; transcription regulator
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.

3d8u__assembly_1__model_1

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

Download this curve (.dat)

3d8u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d8u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.08 Å
Rg (electron density)	24.11 Å
Total Rg	24.86 Å
Atom count	3930
Residues	526
Excluded volume	69438 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d8u__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 (1)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d8ua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.0 — automated matches

Domain ID domain_id	d3d8ub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3d8uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	3d8uA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	3d8uB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	3d8uB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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Unit-cell length a length_a	126.264 Å
Unit-cell length b length_b	126.264 Å
Unit-cell length c length_c	83.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	41.300 Å
R factor r_factor	0.2170
R_work r_work	0.2137
R_free r_free	0.2828

Description description	PurR transcriptional regulator
Molecular weight formula_weight	30523.0 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	3935

The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633

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

PurR transcriptional regulator

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

3d8u__assembly_1__model_1

3d8u__assembly_1__model_1 | I(q)

3d8u__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Vibrio parahaemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	670
Host organism host_organism	Escherichia coli

The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633

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

PurR transcriptional regulator

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

3d8u__assembly_1__model_1

3d8u__assembly_1__model_1 | I(q)

3d8u__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)