2i25

Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme

Method: X-RAY DIFFRACTION Dmax: 87.9 Å Quality: EXCELLENT

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

New Antigen Receptor PBLA8

Ginglymostoma cirratum

UniProt Q8AXH5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain N; UniProt 1–112 Fragment:variable domain Lysozyme C × 1 (P00698) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain O; UniProt 1–112 Fragment:variable domain Lysozyme C × 1 (P00698) 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

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.

1 other PDB entries and 1 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 Author chain O; PDBConstruct 1–112; UniProt 1–112

Lysozyme C

OrganismNot specified

UniProt P00698

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 19–147 Not recorded New Antigen Receptor PBLA8 × 1 (Q8AXH5) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain M; UniProt 19–147 Not recorded New Antigen Receptor PBLA8 × 1 (Q8AXH5) 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

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.

1320 other PDB entries and 1449 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 2
Chains and sequence ranges Author chain L; PDBConstruct 1–129; UniProt 19–147 Author chain M; PDBConstruct 1–129; UniProt 19–147

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2i25

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2i25
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2i25
Deposition date deposition_date2006-08-15
Structure title titleCrystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme
Keywords keywordsimmunoglobulin fold, protein-protein complex, immune system; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.25
Radius of gyration Rg (electron density) rg_electron26.71
Forward intensity I(0) i056142500.00
Molecular weight molecular_weight54036.0 kDa
Excluded volume excluded_volume65854 ų
Envelope volume envelope_volume81837 ų
Hydration-shell volume shell_volume26313 ų
Envelope diameter envelope_diameter94.7
Shell Rg shell_rg32.93
Envelope Rg envelope_rg26.90
Shape Rg shape_rg26.68
Total Rg total_rg27.41
Total atoms total_atoms3784
Residues n_residues489
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.9
Rg (real space) rg_real27.21
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real5.6140e+07
I(0) uncertainty (real space) i0_real_error8.4000e+05
Rg (reciprocal space) rg_reciprocal27.23
I(0) (reciprocal space) i0_reciprocal56140000.0000
Solution quality estimate total_estimate0.9052
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.589
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11130000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2i25l_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme
Domain ID domain_idd2i25m_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme
Domain ID domain_idd2i25n1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i25n2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i25o1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i25o2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id2i25L00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id2i25M00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id2i25N00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i25O00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)