SAXSdb — 1by2

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

MAC-2 BINDING PROTEIN

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 19–133	Fragment：SCAVENGER RECEPTOR CYSTEINE-RICH (SRCR) DOMAIN Mutation：N-TERMINAL APLA	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.00 Å R-free 0.218

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 1BY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GFB Structure of the BTB/POZ domain of human 90K Deposited 2018-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 124–250（127 aa） Chain B 124–250（127 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；9% PEG 8000 0.2M zinc acetate 0.1M imidazole pH 6.8	Resolution 2.08 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	LG3BP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–119； UniProt 19–133

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	1by2
Deposition date deposition_date	1998-10-23
Structure title title	STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN
Keywords keywords	EXTRACELLULAR MODULE, SCAVENGER RECEPTOR, TUMOUR-ASSOCIATED ANTIGEN, EXTRACELLULAR MATRIX, GLYCOSYLATED PROTEIN; EXTRACELLULAR MODULE
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	13.99 Å
Radius of gyration Rg (electron density) rg_electron	12.68 Å
Forward intensity I(0) i0	3534580.00
Molecular weight molecular_weight	12128.0 kDa
Excluded volume excluded_volume	14694 Å³
Envelope volume envelope_volume	16304 Å³
Hydration-shell volume shell_volume	10894 Å³
Envelope diameter envelope_diameter	43.7 Å
Shell Rg shell_rg	18.57 Å
Envelope Rg envelope_rg	13.08 Å
Shape Rg shape_rg	12.67 Å
Total Rg total_rg	13.91 Å
Total atoms total_atoms	846
Residues n_residues	112
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	47.1 Å
Rg (real space) rg_real	13.88 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	3.5350e+06
I(0) uncertainty (real space) i0_real_error	4.0090e+04
Rg (reciprocal space) rg_reciprocal	13.89 Å
I(0) (reciprocal space) i0_reciprocal	3535000.0000
Solution quality estimate total_estimate	0.8674
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.346
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1004000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MAC-2 BINDING PROTEIN
Molecular weight formula_weight	12705.1 kDa
Mutation mutation	N-TERMINAL APLA
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	903

APLAVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNETRSTHTL

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1by2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.170 — SRCR-like
Superfamily Superfamily superfamily	d.170.1 — SRCR-like
Family Family family	d.170.1.1 — Scavenger receptor cysteine-rich (SRCR) domain

Domain ID domain_id	d1by2a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1by2A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	250 — Mac-2 Binding Protein
Homologous superfamily homologous superfamily	10 — SRCR-like domain

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8. Citations (3)

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Unit-cell length a length_a	44.630 Å
Unit-cell length b length_b	44.630 Å
Unit-cell length c length_c	134.540 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2180

fit	/app/data/saxs_computation/by/1by2/1by2.fit
pddf	/app/data/pr_computation/by/1by2/1by2.pr.out
profile	/app/data/saxs_computation/by/1by2/1by2.dat

STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN

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

MAC-2 BINDING PROTEIN

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