SAXSdb — 3dbi

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

SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI FAMILY

Escherichia coli K12

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASCG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–338； UniProt 3–337 Author chain B； PDBConstruct 4–338； UniProt 3–337 Author chain C； PDBConstruct 4–338； UniProt 3–337

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	3dbi
Deposition date deposition_date	2008-06-01
Structure title title	CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE
Keywords keywords	;STRUCTURAL GENOMICS, SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, PROTEIN STRUCTURE INITIATIVE, PSI-2, New York SGX Research Center for Structural Genomics, NYSGXRC, DNA-BINDING, TRANSCRIPTION REGULATION, TRANSCRIPTION REGULATOR, Repressor, Transcription ;; 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.

3dbi__assembly_1__model_1

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

Download this curve (.dat)

3dbi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dbi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.02 Å
Rg (electron density)	24.90 Å
Total Rg	25.67 Å
Atom count	4288
Residues	537
Excluded volume	76731 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dbi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dbi__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	SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI FAMILY
Molecular weight formula_weight	37574.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6617

MSLTTMLEVAKRAGVSKATVSRVLSGNGYVSQETKDRVFQAVEESGYRPNLLARNLSAKSTQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIAPSR

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	119

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3dbia_
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	d3dbib_
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	d3dbic_
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 (6 domains)

Domain ID domain_id	3dbiA01
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	3dbiA02
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	3dbiB01
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	3dbiB02
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	3dbiC01
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	3dbiC02
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	82.468 Å
Unit-cell length b length_b	82.468 Å
Unit-cell length c length_c	341.448 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2321
R_work r_work	0.2309
R_free r_free	0.2704

CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE

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

SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI 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

3dbi__assembly_1__model_1

3dbi__assembly_1__model_1 | I(q)

3dbi__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE

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

SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI 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

3dbi__assembly_1__model_1

3dbi__assembly_1__model_1 | I(q)

3dbi__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)