SAXSdb — 3r8k

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

Heme-binding protein 2

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–205	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–205	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2–205	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 2–205	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268

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 3R8K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R8J Crystal structure of human SOUL protein (orthorhombic form) Deposited 2011-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–205（204 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；KH2PO4 0.8M, NaH2PO4 0.8M, HEPES 0.08M, 1-butyl-3-methylimidazolium chloride 0.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.197
3R8J Crystal structure of human SOUL protein (orthorhombic form) Deposited 2011-03-24	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；KH2PO4 0.8M, NaH2PO4 0.8M, HEPES 0.08M, 1-butyl-3-methylimidazolium chloride 0.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.197
4AYZ X-ray Structure of human SOUL Deposited 2012-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.8 M NA/K PHOSPHATE BUFFER 5.6	Resolution 3.50 Å R-free 0.270
4B0Y Determination of X-ray Structure of human SOUL by Molecular Replacement Deposited 2012-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；2 M AMMONIUM SULPHATE, 0.1 M MES 6.5	Resolution 3.50 Å R-free 0.306
5GQQ Structure of ALG-2/HEBP2 Complex Deposited 2016-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–197（178 aa） Fragment：UNP RESIDUES 20-197 Chain B 20–197（178 aa） Fragment：UNP RESIDUES 20-197	Not recorded	CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M Bis-Tris, 2 M NaCl, pH 5.5	Resolution 2.20 Å R-free 0.225

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HEBP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–208； UniProt 2–205 Author chain B； PDBConstruct 5–208； UniProt 2–205 Author chain C； PDBConstruct 5–208； UniProt 2–205 Author chain D； PDBConstruct 5–208； UniProt 2–205

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	3r8k
Deposition date deposition_date	2011-03-24
Structure title title	Crystal structure of human SOUL protein (hexagonal form)
Keywords keywords	HEBP family, SOUL protein, APOPTOSIS; APOPTOSIS
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	41.89 Å
Radius of gyration Rg (electron density) rg_electron	42.66 Å
Forward intensity I(0) i0	97210900.00
Molecular weight molecular_weight	79724.0 kDa
Excluded volume excluded_volume	99856 Å³
Envelope volume envelope_volume	147520 Å³
Hydration-shell volume shell_volume	33798 Å³
Envelope diameter envelope_diameter	147.7 Å
Shell Rg shell_rg	39.35 Å
Envelope Rg envelope_rg	42.23 Å
Shape Rg shape_rg	42.61 Å
Total Rg total_rg	42.59 Å
Total atoms total_atoms	5631
Residues n_residues	706
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	140.2 Å
Rg (real space) rg_real	42.45 Å
Rg uncertainty (real space) rg_real_error	1.70 Å
I(0) (real space) i0_real	9.7210e+07
I(0) uncertainty (real space) i0_real_error	1.7690e+06
Rg (reciprocal space) rg_reciprocal	41.89 Å
I(0) (reciprocal space) i0_reciprocal	97150000.0000
Solution quality estimate total_estimate	0.6843
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	59.0 Å
Skewness Skewness skewness	0.610
Kurtosis Kurtosis kurtosis	-0.058
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5866000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.395; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.645; Smooth: 0.061

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3r8ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.0 — automated matches

Domain ID domain_id	d3r8kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.0 — automated matches

Domain ID domain_id	d3r8kc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.0 — automated matches

Domain ID domain_id	d3r8kd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3r8kA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	3r8kB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	3r8kC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	3r8kD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

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8. Citations (1)

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Unit-cell length a length_a	143.919 Å
Unit-cell length b length_b	143.919 Å
Unit-cell length c length_c	242.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	55.400 Å
R factor r_factor	0.2367
R_work r_work	0.2350
R_free r_free	0.2683

Description description	Heme-binding protein 2
Molecular weight formula_weight	23663.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5631

Crystal structure of human SOUL protein (hexagonal form)

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

Heme-binding protein 2

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/r8/3r8k/3r8k.fit
pddf	/app/data/pr_computation/r8/3r8k/3r8k.pr.out
profile	/app/data/saxs_computation/r8/3r8k/3r8k.dat