SAXSdb — 8iw5

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

Liprin-beta-1

Mus musculus

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 43–89 Chain B； UniProt 43–89	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.05 M Calcium acetate, 0.1 M Sodium cacodylate pH 6.0 and 25% v/v MPD	Resolution 1.70 Å R-free 0.272

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 8IW5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 593–853（261 aa） Fragment：UNP residues 593-853	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 593–853（261 aa） Fragment：UNP residues 593-853	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
8IW0 Crystal structure of the KANK1/liprin-beta1 complex Deposited 2023-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–23（23 aa） Fragment：N-terminal,N-terminal Chain B 1–23（23 aa） Fragment：N-terminal,N-terminal	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 2.10 Å R-free 0.259
8IW0 Crystal structure of the KANK1/liprin-beta1 complex Deposited 2023-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–23（23 aa） Fragment：N-terminal,N-terminal Chain D 1–23（23 aa） Fragment：N-terminal,N-terminal	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 2.10 Å R-free 0.259

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIPB1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–51； UniProt 43–89 Author chain B； PDBConstruct 5–51； UniProt 43–89

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	8iw5
Deposition date deposition_date	2023-03-29
Structure title title	Crystal structure of liprin-beta H2H3 dimer
Keywords keywords	Focal adhesion, Cortical microtubule stabilizing complex, PROTEIN BINDING; PROTEIN BINDING
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	14.21 Å
Radius of gyration Rg (electron density) rg_electron	12.49 Å
Forward intensity I(0) i0	2380080.00
Molecular weight molecular_weight	10271.0 kDa
Excluded volume excluded_volume	12759 Å³
Envelope volume envelope_volume	14494 Å³
Hydration-shell volume shell_volume	10096 Å³
Envelope diameter envelope_diameter	45.7 Å
Shell Rg shell_rg	17.89 Å
Envelope Rg envelope_rg	12.74 Å
Shape Rg shape_rg	12.43 Å
Total Rg total_rg	13.92 Å
Total atoms total_atoms	714
Residues n_residues	92
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	45.8 Å
Rg (real space) rg_real	14.11 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.3800e+06
I(0) uncertainty (real space) i0_real_error	2.3510e+04
Rg (reciprocal space) rg_reciprocal	14.11 Å
I(0) (reciprocal space) i0_reciprocal	2380000.0000
Solution quality estimate total_estimate	0.7946
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.134
Kurtosis Kurtosis kurtosis	-0.206
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	462300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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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	Liprin-beta-1
Molecular weight formula_weight	5715.5 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	770

GPGSMGSLRALHLVEDLRGLLEMMETDEKEGLRCQIPDSTAEVLIEWLQNQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
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	39

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8. Citations (1)

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Unit-cell length a length_a	29.793 Å
Unit-cell length b length_b	50.637 Å
Unit-cell length c length_c	30.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	27.330 Å
R factor r_factor	0.2236
R_work r_work	0.2210
R_free r_free	0.2717

fit	/app/data/saxs_computation/iw/8iw5/8iw5.fit
pddf	/app/data/pr_computation/iw/8iw5/8iw5.pr.out
profile	/app/data/saxs_computation/iw/8iw5/8iw5.dat

Crystal structure of liprin-beta H2H3 dimer

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

Liprin-beta-1

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