1sq2

Crystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme

Method: X-RAY DIFFRACTION Dmax: 82.4 Å Quality: GOOD

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

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 novel antigen receptor × 1 (Q8AXI4) CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;15% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K Resolution 1.45 Å R-free 0.225

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 1450 assemblies. Open the comparison page and filter oligomeric states

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

novel antigen receptor

Ginglymostoma cirratum

UniProt Q8AXI4

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 1–113 Not recorded Lysozyme C × 1 (P00698) CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;15% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K Resolution 1.45 Å R-free 0.225

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 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8AXI4_GINCI
Isoform
PDB entities 2
Chains and sequence ranges Author chain N; PDBConstruct 1–113; UniProt 1–113

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 1sq2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1sq2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1sq2
Deposition date deposition_date2004-03-17
Structure title titleCrystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme
Keywords keywordsimmunoglobulin fold, protein-protein complex, HYDROLASE-IMMUNE SYSTEM COMPLEX; HYDROLASE/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.93
Radius of gyration Rg (electron density) rg_electron20.41
Forward intensity I(0) i014576700.00
Molecular weight molecular_weight26603.0 kDa
Excluded volume excluded_volume32377 ų
Envelope volume envelope_volume38168 ų
Hydration-shell volume shell_volume16761 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg25.61
Envelope Rg envelope_rg20.68
Shape Rg shape_rg20.38
Total Rg total_rg21.17
Total atoms total_atoms1856
Residues n_residues241
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 dmax82.4
Rg (real space) rg_real21.06
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real1.4580e+07
I(0) uncertainty (real space) i0_real_error1.8260e+05
Rg (reciprocal space) rg_reciprocal21.03
I(0) (reciprocal space) i0_reciprocal14580000.0000
Solution quality estimate total_estimate0.7638
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.532
Kurtosis Kurtosis kurtosis-0.116
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4543000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.472; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1sq2l_
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_idd1sq2n_
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)

CATH v4.4 (2 domains)

Domain ID domain_id1sq2L00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id1sq2N00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)