SAXSdb — 3brj

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

Mannitol operon repressor

Vibrio parahaemolyticus RIMD 2210633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87SQ4_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–175； UniProt 1–172 Author chain B； PDBConstruct 4–175； UniProt 1–172 Author chain C； PDBConstruct 4–175； UniProt 1–172 Author chain D； PDBConstruct 4–175； UniProt 1–172

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	3brj
Deposition date deposition_date	2007-12-21
Structure title title	Crystal structure of mannitol operon repressor (MtlR) from Vibrio parahaemolyticus RIMD 2210633
Keywords keywords	;APC85967.1, mannitol operon repressor, MtlR, Vibrio parahaemolyticus RIMD 2210633, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

3brj__assembly_1__model_1

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

Download this curve (.dat)

3brj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3brj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.82 Å
Rg (electron density)	29.77 Å
Total Rg	29.86 Å
Atom count	2686
Residues	332
Excluded volume	48269 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3brj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3brj__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Mannitol operon repressor
Molecular weight formula_weight	19838.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5361

SNAMADNINESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKMGMVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK

Source Source

Source organism organism	Vibrio parahaemolyticus RIMD 2210633
NCBI taxonomy ID ncbi_taxonomy_id	223926
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	30

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3brja1
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3brjb_
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3brjc_
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3brjd_
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

CATH v4.4 (4 domains)

Domain ID domain_id	3brjA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3brjB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3brjC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3brjD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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Unit-cell length a length_a	63.281 Å
Unit-cell length b length_b	63.281 Å
Unit-cell length c length_c	227.100 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	16

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	48.560 Å
R factor r_factor	0.2101
R_work r_work	0.2068
R_free r_free	0.2727

Crystal structure of mannitol operon repressor (MtlR) from Vibrio parahaemolyticus RIMD 2210633

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

Mannitol operon repressor

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

3brj__assembly_1__model_1

3brj__assembly_1__model_1 | I(q)

3brj__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of mannitol operon repressor (MtlR) from Vibrio parahaemolyticus RIMD 2210633

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

Mannitol operon repressor

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

3brj__assembly_1__model_1

3brj__assembly_1__model_1 | I(q)

3brj__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)