SAXSdb — 9dkz

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

Bone marrow proteoglycan

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 107–222	Not recorded	No other associated polymer	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer：pH 7；secretory granule matrix cryo-EM vitrification conditions：Cryogen ETHANE；Blot time of 6~8 sec, single-side back blotting	Resolution 3.20 Å R-free 0.311

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 9DKZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H8U Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity Deposited 2001-02-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100MM MALONIC ACID PH6, 140MM POTTASIUM DIHYDROGEN PHOSPHATE., pH 6.00	Resolution 1.80 Å R-free 0.264
1H8U Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity Deposited 2001-02-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100MM MALONIC ACID PH6, 140MM POTTASIUM DIHYDROGEN PHOSPHATE., pH 6.00	Resolution 1.80 Å R-free 0.264
2BRS EMBP Heparin complex Deposited 2005-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.291
2BRS EMBP Heparin complex Deposited 2005-05-11	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.291
4QXX Structure of the amyloid forming peptide GNLVS (residues 26-30) from the eosinophil major basic protein (EMBP) Deposited 2014-07-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain Z 131–135（5 aa） Fragment：GNLVS peptide (UNP residues 131-135)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；291 K；2 M ammonium sulfate, 0.1 M phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.45 Å R-free 0.192
7Y5N Structure of 1:1 PAPP-A.ProMBP complex(half map) Deposited 2022-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–222（222 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 1 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
8HGG Structure of 2:2 PAPP-A.ProMBP complex Deposited 2022-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.64 Å
9PPV In situ MicroED structure of human eosinophil major basic protein-1 Deposited 2025-07-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å R-free 0.313
9PPV In situ MicroED structure of human eosinophil major basic protein-1 Deposited 2025-07-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å R-free 0.313
9PSE In situ MicroED structure of IL-5 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 107–222（116 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested from human donor peripheral blood and rested in 1640 RPMI medium supplemented with 0.1% human serum albumin (HSA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.320
9PSE In situ MicroED structure of IL-5 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–222（116 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested from human donor peripheral blood and rested in 1640 RPMI medium supplemented with 0.1% human serum albumin (HSA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.320
9PSK In situ MicroED structure of IL-33 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–222（117 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested eosinophiles resting in 1640 RPMI medium (Sigma-Aldrich) supplemented with 0.1% human serum albumin (HSA) (Sigma-Aldrich) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.340
9PSK In situ MicroED structure of IL-33 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested eosinophiles resting in 1640 RPMI medium (Sigma-Aldrich) supplemented with 0.1% human serum albumin (HSA) (Sigma-Aldrich) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.340

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRG2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 107–222

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	9dkz
Deposition date deposition_date	2024-09-10
Structure title title	In situ microED structure of the Eosinophil major basic protein-1
Keywords keywords	Effector, Nanocrystal, In-situ, Intracellular, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON CRYSTALLOGRAPHY

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

Radius of gyration Rg (Guinier) rg_guinier	15.13 Å
Radius of gyration Rg (electron density) rg_electron	13.51 Å
Forward intensity I(0) i0	4174830.00
Molecular weight molecular_weight	13689.0 kDa
Excluded volume excluded_volume	16841 Å³
Envelope volume envelope_volume	19172 Å³
Hydration-shell volume shell_volume	11966 Å³
Envelope diameter envelope_diameter	51.1 Å
Shell Rg shell_rg	19.51 Å
Envelope Rg envelope_rg	14.06 Å
Shape Rg shape_rg	13.44 Å
Total Rg total_rg	14.93 Å
Total atoms total_atoms	1889
Residues n_residues	116
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	50.7 Å
Rg (real space) rg_real	15.03 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	4.1750e+06
I(0) uncertainty (real space) i0_real_error	4.9830e+04
Rg (reciprocal space) rg_reciprocal	15.04 Å
I(0) (reciprocal space) i0_reciprocal	4175000.0000
Solution quality estimate total_estimate	0.8597
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.185
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1219000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.986

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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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8. Citations (1)

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Unit-cell length a length_a	31.240 Å
Unit-cell length b length_b	57.870 Å
Unit-cell length c length_c	59.060 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	28.930 Å
R factor r_factor	0.2727
R_work r_work	0.2679
R_free r_free	0.3110

Resolution resolution	3.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	—

Description description	Bone marrow proteoglycan
Molecular weight formula_weight	13694.8 kDa
Source method src_method	man
Copy count entity_count	1

In situ microED structure of the Eosinophil major basic protein-1

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

Bone marrow proteoglycan

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1890

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	Homo sapiens

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

fit	/app/data/saxs_computation/dk/9dkz/9dkz.fit
pddf	/app/data/pr_computation/dk/9dkz/9dkz.pr.out
profile	/app/data/saxs_computation/dk/9dkz/9dkz.dat