SAXSdb — 1bg8

▼

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

HDEA

OrganismNot specified

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 22–110 Chain B； UniProt 22–110	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.6；36% PEG400, 5% GLYCEROL, 50MM SODIUM CITRATE, PH 3.6	Resolution 2.20 Å R-free 0.278
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 22–110	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.6；36% PEG400, 5% GLYCEROL, 50MM SODIUM CITRATE, PH 3.6	Resolution 2.20 Å R-free 0.278

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 1BG8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJ8 CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA Deposited 1999-12-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–110（89 aa） Chain B 22–110（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.261
1DJ8 CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA Deposited 1999-12-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 22–110（89 aa） Chain D 22–110（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.261
1DJ8 CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA Deposited 1999-12-02	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 22–110（89 aa） Chain F 22–110（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.261

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HDEA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 22–110 Author chain B； PDBConstruct 1–89； UniProt 22–110 Author chain C； PDBConstruct 1–89； UniProt 22–110

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bg8
Deposition date deposition_date	1998-06-05
Structure title title	HDEA FROM ESCHERICHIA COLI
Keywords keywords	PERIPLASMIC, HDEA; PERIPLASMIC
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.06 Å
Radius of gyration Rg (electron density) rg_electron	27.76 Å
Forward intensity I(0) i0	10576100.00
Molecular weight molecular_weight	24997.0 kDa
Excluded volume excluded_volume	31273 Å³
Envelope volume envelope_volume	43351 Å³
Hydration-shell volume shell_volume	14061 Å³
Envelope diameter envelope_diameter	91.2 Å
Shell Rg shell_rg	32.55 Å
Envelope Rg envelope_rg	26.99 Å
Shape Rg shape_rg	27.71 Å
Total Rg total_rg	28.47 Å
Total atoms total_atoms	1761
Residues n_residues	228
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	87.0 Å
Rg (real space) rg_real	28.44 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	1.0580e+07
I(0) uncertainty (real space) i0_real_error	1.5820e+05
Rg (reciprocal space) rg_reciprocal	28.34 Å
I(0) (reciprocal space) i0_reciprocal	10580000.0000
Solution quality estimate total_estimate	0.6684
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.299
Kurtosis Kurtosis kurtosis	-1.149
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1290000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.203; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.185; Smooth: 0.891

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1bg8a_
Class class	a — All alpha proteins
Fold Fold fold	a.57 — Protein HNS-dependent expression A; HdeA
Superfamily Superfamily superfamily	a.57.1 — Protein HNS-dependent expression A; HdeA
Family Family family	a.57.1.1 — Protein HNS-dependent expression A; HdeA

Domain ID domain_id	d1bg8b_
Class class	a — All alpha proteins
Fold Fold fold	a.57 — Protein HNS-dependent expression A; HdeA
Superfamily Superfamily superfamily	a.57.1 — Protein HNS-dependent expression A; HdeA
Family Family family	a.57.1.1 — Protein HNS-dependent expression A; HdeA

Domain ID domain_id	d1bg8c_
Class class	a — All alpha proteins
Fold Fold fold	a.57 — Protein HNS-dependent expression A; HdeA
Superfamily Superfamily superfamily	a.57.1 — Protein HNS-dependent expression A; HdeA
Family Family family	a.57.1.1 — Protein HNS-dependent expression A; HdeA

CATH v4.4 (3 domains)

Domain ID domain_id	1bg8A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	890 — 10k-s Protein, Hypothetical Protein A; Chain A
Homologous superfamily homologous superfamily	10 — HNS-dependent expression A

Domain ID domain_id	1bg8B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	890 — 10k-s Protein, Hypothetical Protein A; Chain A
Homologous superfamily homologous superfamily	10 — HNS-dependent expression A

Domain ID domain_id	1bg8C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	890 — 10k-s Protein, Hypothetical Protein A; Chain A
Homologous superfamily homologous superfamily	10 — HNS-dependent expression A

▶

8. Citations (1)

▶

Unit-cell length a length_a	47.476 Å
Unit-cell length b length_b	76.149 Å
Unit-cell length c length_c	73.607 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1630
R_work r_work	0.1630
R_free r_free	0.2780

Description description	HDEA
Molecular weight formula_weight	9752.9 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1988

HDEA FROM ESCHERICHIA COLI

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

HDEA

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	227

fit	/app/data/saxs_computation/bg/1bg8/1bg8.fit
pddf	/app/data/pr_computation/bg/1bg8/1bg8.pr.out
profile	/app/data/saxs_computation/bg/1bg8/1bg8.dat