SAXSdb — 1dj8

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

PROTEIN HNS-DEPENDENT EXPRESSION A

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：VAPOR DIFFUSION；pH 4；298 K；PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.261
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 22–110 Chain D； UniProt 22–110	Not recorded	No other associated polymer	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 22–110 Chain F； UniProt 22–110	Not recorded	No other associated polymer	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

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 1DJ8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BG8 HDEA FROM ESCHERICHIA COLI Deposited 1998-06-05	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 pH 3.6；36% PEG400, 5% GLYCEROL, 50MM SODIUM CITRATE, PH 3.6	Resolution 2.20 Å R-free 0.278
1BG8 HDEA FROM ESCHERICHIA COLI Deposited 1998-06-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 22–110（89 aa）	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 2 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 Author chain D； PDBConstruct 1–89； UniProt 22–110 Author chain E； PDBConstruct 1–89； UniProt 22–110 Author chain F； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dj8
Deposition date deposition_date	1999-12-02
Structure title title	CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA
Keywords keywords	ALPHA HELICAL, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.67 Å
Radius of gyration Rg (electron density) rg_electron	28.83 Å
Forward intensity I(0) i0	45025600.00
Molecular weight molecular_weight	52229.0 kDa
Excluded volume excluded_volume	65413 Å³
Envelope volume envelope_volume	87788 Å³
Hydration-shell volume shell_volume	25923 Å³
Envelope diameter envelope_diameter	96.7 Å
Shell Rg shell_rg	35.13 Å
Envelope Rg envelope_rg	28.36 Å
Shape Rg shape_rg	28.79 Å
Total Rg total_rg	29.61 Å
Total atoms total_atoms	3678
Residues n_residues	474
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

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

Maximum dimension Dmax dmax	91.1 Å
Rg (real space) rg_real	29.63 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	4.5030e+07
I(0) uncertainty (real space) i0_real_error	6.3920e+05
Rg (reciprocal space) rg_reciprocal	29.65 Å
I(0) (reciprocal space) i0_reciprocal	45030000.0000
Solution quality estimate total_estimate	0.9063
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.142
Kurtosis Kurtosis kurtosis	-0.753
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7806000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.917

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dj8a_
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	d1dj8b_
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	d1dj8c_
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	d1dj8d_
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	d1dj8e_
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	d1dj8f_
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 (6 domains)

Domain ID domain_id	1dj8A00
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	1dj8B00
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	1dj8C00
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	1dj8D00
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	1dj8E00
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	1dj8F00
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

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8. Citations (6)

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Unit-cell length a length_a	47.000 Å
Unit-cell length b length_b	73.600 Å
Unit-cell length c length_c	74.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2610

Description description	PROTEIN HNS-DEPENDENT EXPRESSION A
Molecular weight formula_weight	9752.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4067

CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA

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

PROTEIN HNS-DEPENDENT EXPRESSION A

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (6)

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	389

fit	/app/data/saxs_computation/dj/1dj8/1dj8.fit
pddf	/app/data/pr_computation/dj/1dj8/1dj8.pr.out
profile	/app/data/saxs_computation/dj/1dj8/1dj8.dat