SAXSdb — 6gfb

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

Galectin-3-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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 124–250 Chain B； UniProt 124–250	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

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 6GFB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BY2 STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN Deposited 1998-10-23	Different construct Different mutation/modification 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 19–133（115 aa） 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

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 3–129； UniProt 124–250 Author chain B； PDBConstruct 3–129； UniProt 124–250

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	6gfb
Deposition date deposition_date	2018-04-29
Structure title title	Structure of the BTB/POZ domain of human 90K
Keywords keywords	BTB/POZ domain, 90K, HIV restriction factor, ANTIVIRAL PROTEIN; ANTIVIRAL 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	21.31 Å
Radius of gyration Rg (electron density) rg_electron	20.61 Å
Forward intensity I(0) i0	13484300.00
Molecular weight molecular_weight	26691.0 kDa
Excluded volume excluded_volume	33092 Å³
Envelope volume envelope_volume	39936 Å³
Hydration-shell volume shell_volume	17348 Å³
Envelope diameter envelope_diameter	74.0 Å
Shell Rg shell_rg	25.94 Å
Envelope Rg envelope_rg	20.91 Å
Shape Rg shape_rg	20.54 Å
Total Rg total_rg	21.58 Å
Total atoms total_atoms	1863
Residues n_residues	242
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	73.5 Å
Rg (real space) rg_real	21.42 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.3480e+07
I(0) uncertainty (real space) i0_real_error	1.8520e+05
Rg (reciprocal space) rg_reciprocal	21.40 Å
I(0) (reciprocal space) i0_reciprocal	13480000.0000
Solution quality estimate total_estimate	0.8454
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.505
Kurtosis Kurtosis kurtosis	-0.200
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3009000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.930

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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	Galectin-3-binding protein
Molecular weight formula_weight	18086.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1905

RSTNETRSTHTLDLSRELSEALGQIFDSQRGCDLSISVNVQGEDALGFCGHTVILTANLEAQALWKEPGSNVTMSVDAECVPMVRDLLRYFYSRRIDITLSSVKCFHKLASAYGARQLQGYCASLFAILSRDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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	Drosophila melanogaster

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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8. Citations (1)

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Unit-cell length a length_a	70.340 Å
Unit-cell length b length_b	70.340 Å
Unit-cell length c length_c	105.510 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	20.770 Å
R factor r_factor	0.2099
R_work r_work	0.2082
R_free r_free	0.2433

fit	/app/data/saxs_computation/gf/6gfb/6gfb.fit
pddf	/app/data/pr_computation/gf/6gfb/6gfb.pr.out
profile	/app/data/saxs_computation/gf/6gfb/6gfb.dat

Structure of the BTB/POZ domain of human 90K

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

Galectin-3-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