SAXSdb — 7sbd

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

Profilin-2

Hevea brasiliensis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–131	Not recorded	Fab/IgE Heavy chain × 1 Fab/IgE Light chain × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；2% Tacsimate, pH 6.0, 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG3350	Resolution 3.04 Å R-free 0.254

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 7SBD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FDS Crystal structure of the monomeric allergen profilin (Hev b 8) Deposited 2015-12-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.1M TRIS-HCL, pH 9.0, 1.6 M Ammonium Sulfate	Resolution 1.90 Å R-free 0.197
5FEG Crystal structure of the dimeric allergen profilin (Hev b 8) Deposited 2015-12-17	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 1–131（131 aa） Chain B 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1M TRIS-HCl, pH 9.0; 2.0 M Ammonium Sulfate	Resolution 2.80 Å R-free 0.250
7SBG Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8) Deposited 2021-09-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；291 K；0.2 M lithium acetate, 20% PEG3350	Resolution 3.34 Å R-free 0.298

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

View Construct and Data Evidence

UniProt name	PROF2_HEVBR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–135； UniProt 1–131

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	7sbd
Deposition date deposition_date	2021-09-24
Structure title title	Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8)
Keywords keywords	Antibody, Allergen, IgE/Fab fragment, complex, ALLERGEN-IMMUNE SYSTEM complex; ALLERGEN/IMMUNE SYSTEM
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	29.39 Å
Radius of gyration Rg (electron density) rg_electron	29.13 Å
Forward intensity I(0) i0	57290700.00
Molecular weight molecular_weight	57831.0 kDa
Excluded volume excluded_volume	71455 Å³
Envelope volume envelope_volume	92155 Å³
Hydration-shell volume shell_volume	28365 Å³
Envelope diameter envelope_diameter	105.9 Å
Shell Rg shell_rg	34.14 Å
Envelope Rg envelope_rg	29.14 Å
Shape Rg shape_rg	29.10 Å
Total Rg total_rg	29.68 Å
Total atoms total_atoms	4077
Residues n_residues	558
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	101.3 Å
Rg (real space) rg_real	29.64 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	5.7290e+07
I(0) uncertainty (real space) i0_real_error	9.7480e+05
Rg (reciprocal space) rg_reciprocal	29.54 Å
I(0) (reciprocal space) i0_reciprocal	57290000.0000
Solution quality estimate total_estimate	0.8394
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.0 Å
Skewness Skewness skewness	0.586
Kurtosis Kurtosis kurtosis	-0.101
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10720000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.741

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fab/IgE Heavy chain
Molecular weight formula_weight	23226.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4077

EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRTKTNNYVTYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRHVGDYWGQGTSVTVSSASIRNPQLYPLKPCKGTASMTLGCLVKDYFPGPVTVTWYSDSLNMSTVNFPALGSELKVTTSQVTSWGKSAKNFTCHVTHPPSFNESRTILVR

Entity 2 Entity 2 polymer

Description description	Fab/IgE Light chain
Molecular weight formula_weight	23616.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWFQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 3 Entity 3 polymer

Description description	Profilin-2
Molecular weight formula_weight	14636.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DDDKMSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTLAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVERLGDYLIDQGY

来源 Source

来源生物 organism	Hevea brasiliensis
通用名 common_name	rubber tree
NCBI Class编号 ncbi_taxonomy_id	3981
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7sbdH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7sbdH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7sbdL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7sbdL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	57.962 Å
Unit-cell length b length_b	77.468 Å
Unit-cell length c length_c	144.550 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	orthorhombic

Resolution resolution	3.040 Å
Low-resolution limit resolution_low	29.420 Å
R factor r_factor	0.2302
R_work r_work	0.2276
R_free r_free	0.2535

fit	/app/data/saxs_computation/sb/7sbd/7sbd.fit
pddf	/app/data/pr_computation/sb/7sbd/7sbd.pr.out
profile	/app/data/saxs_computation/sb/7sbd/7sbd.dat

Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8)

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

Profilin-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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)