SAXSdb — 8q1d

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

Beta-phosphoglucomutase

Lactococcus lactis subsp. lactis Il1403

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,6-di-O-phosphono-beta-D-fructofuranose × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGMB_LACLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 1–221

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	8q1d
Deposition date deposition_date	2023-07-31
Last revision last_revision	2024-08-07
Structure title title	D10N variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate
Keywords keywords	mutase, complex, ISOMERASE; ISOMERASE
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.

8q1d__assembly_1__model_1

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

Download this curve (.dat)

8q1d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8q1d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.81 Å
Rg (electron density)	17.94 Å
Total Rg	18.93 Å
Atom count	1741
Residues	221
Excluded volume	31156 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8q1d__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Beta-phosphoglucomutase
Molecular weight formula_weight	24238.6 kDa
EC 编号 ec_number	5.4.2.6
Mutation mutation	D10N
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	1940

MFKAVLFDLNGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQKQK

Source Source

Source organism organism	Lactococcus lactis subsp. lactis Il1403
NCBI taxonomy ID ncbi_taxonomy_id	272623
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,6-di-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	340.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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Unit-cell length a length_a	31.888 Å
Unit-cell length b length_b	71.382 Å
Unit-cell length c length_c	83.909 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	54.429 Å
R factor r_factor	—
R_work r_work	0.1610
R_free r_free	0.2520

D10N variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate

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

Beta-phosphoglucomutase

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

8q1d__assembly_1__model_1

8q1d__assembly_1__model_1 | I(q)

8q1d__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

D10N variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate

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

Beta-phosphoglucomutase

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

8q1d__assembly_1__model_1

8q1d__assembly_1__model_1 | I(q)

8q1d__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)