SAXSdb — 2i24

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

New Antigen Receptor PBLA8

Ginglymostoma cirratum

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 N； UniProt 1–112	Fragment：variable domain	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；24% PEG 400, 0.1M Na/K phosphate, 0.15M NaCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.35 Å R-free 0.214

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 2I24	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2I25 Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme Deposited 2006-08-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 1–112（112 aa） Fragment：variable domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；295 K；38% PEG 400, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.211
2I25 Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme Deposited 2006-08-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–112（112 aa） Fragment：variable domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；295 K；38% PEG 400, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.211

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

View Construct and Data Evidence

UniProt name	Q8AXH5_GINCI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain N； PDBConstruct 1–112； UniProt 1–112

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	2i24
Deposition date deposition_date	2006-08-15
Structure title title	Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain
Keywords keywords	immunoglobulin fold, immune system; 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	15.62 Å
Radius of gyration Rg (electron density) rg_electron	14.63 Å
Forward intensity I(0) i0	3624590.00
Molecular weight molecular_weight	12472.0 kDa
Excluded volume excluded_volume	15212 Å³
Envelope volume envelope_volume	17820 Å³
Hydration-shell volume shell_volume	10943 Å³
Envelope diameter envelope_diameter	56.0 Å
Shell Rg shell_rg	19.51 Å
Envelope Rg envelope_rg	15.04 Å
Shape Rg shape_rg	14.60 Å
Total Rg total_rg	15.68 Å
Total atoms total_atoms	873
Residues n_residues	113
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	58.3 Å
Rg (real space) rg_real	15.63 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	3.6250e+06
I(0) uncertainty (real space) i0_real_error	4.2800e+04
Rg (reciprocal space) rg_reciprocal	15.63 Å
I(0) (reciprocal space) i0_reciprocal	3625000.0000
Solution quality estimate total_estimate	0.8160
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.404
Kurtosis Kurtosis kurtosis	-0.174
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	791300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.604; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.792; 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	New Antigen Receptor PBLA8
Molecular weight formula_weight	13437.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N
Atom count atom_count	1028

ARVDQTPQRITKETGESLTINCVVRDSRCVLSTGYWYRKPPGSRNEESISDGGRYVETVNRGSKSFSLRINDLTVKDSGTYRCKPESRYGSYDAVCAALNDQYGGGTVVTVNAAAHHHHHH

来源 Source

来源生物 organism	Ginglymostoma cirratum
通用名 common_name	nurse shark
NCBI Class编号 ncbi_taxonomy_id	7801
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	155

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2i24n1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2i24n2
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	2i24N00
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	53.958 Å
Unit-cell length b length_b	53.958 Å
Unit-cell length c length_c	79.077 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	1.350 Å
Low-resolution limit resolution_low	44.700 Å
R factor r_factor	0.1741
R_work r_work	0.1721
R_free r_free	0.2143

fit	/app/data/saxs_computation/i2/2i24/2i24.fit
pddf	/app/data/pr_computation/i2/2i24/2i24.pr.out
profile	/app/data/saxs_computation/i2/2i24/2i24.dat

Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain

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

New Antigen Receptor PBLA8

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