1gpr

REFINED CRYSTAL STRUCTURE OF IIA DOMAIN OF THE GLUCOSE PERMEASE OF BACILLUS SUBTILIS AT 1.9 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 50.5 Å Quality: GOOD

▼

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

GLUCOSE PERMEASE

Bacillus subtilis

UniProt P20166

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–162	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1GPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AX3 SOLUTION NMR STRUCTURE OF B. SUBTILIS IIAGLC, 16 STRUCTURES Deposited 1997-10-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–162（162 aa） Fragment：A DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.87；308 K	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTG3C_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gpr
Deposition date deposition_date	1991-09-25
Structure title title	REFINED CRYSTAL STRUCTURE OF IIA DOMAIN OF THE GLUCOSE PERMEASE OF BACILLUS SUBTILIS AT 1.9 ANGSTROMS RESOLUTION
Keywords keywords	PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.15 Å
Radius of gyration Rg (electron density) rg_electron	14.56 Å
Forward intensity I(0) i0	5345040.00
Molecular weight molecular_weight	16907.0 kDa
Excluded volume excluded_volume	21320 Å³
Envelope volume envelope_volume	23771 Å³
Hydration-shell volume shell_volume	13709 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	20.60 Å
Envelope Rg envelope_rg	14.84 Å
Shape Rg shape_rg	14.55 Å
Total Rg total_rg	15.80 Å
Total atoms total_atoms	1191
Residues n_residues	158
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	50.5 Å
Rg (real space) rg_real	16.02 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	5.3450e+06
I(0) uncertainty (real space) i0_real_error	6.0190e+04
Rg (reciprocal space) rg_reciprocal	16.04 Å
I(0) (reciprocal space) i0_reciprocal	5345000.0000
Solution quality estimate total_estimate	0.8084
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.088
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1230000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1gpra_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.3 — Duplicated hybrid motif
Family Family family	b.84.3.1 — Glucose permease-like

CATH v4.4 (1 domains)

Domain ID domain_id	1gprA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	70 — Glucose Permease (Domain IIA)
Homologous superfamily homologous superfamily	10 — Glucose Permease (Domain IIA)

▶

8. Citations (4)

▶

Unit-cell length a length_a	74.220 Å
Unit-cell length b length_b	54.940 Å
Unit-cell length c length_c	66.960 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1560
R_work r_work	—
R_free r_free	—

Description description	GLUCOSE PERMEASE
Molecular weight formula_weight	17396.8 kDa
EC 编号 ec_number	2.7.1.69
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1291

REFINED CRYSTAL STRUCTURE OF IIA DOMAIN OF THE GLUCOSE PERMEASE OF BACILLUS SUBTILIS AT 1.9 ANGSTROMS RESOLUTION

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

GLUCOSE PERMEASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

fit	/app/data/saxs_computation/gp/1gpr/1gpr.fit
pddf	/app/data/pr_computation/gp/1gpr/1gpr.pr.out
profile	/app/data/saxs_computation/gp/1gpr/1gpr.dat