2i26

Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme

Method: X-RAY DIFFRACTION Dmax: 108.5 Å Quality: GOOD

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

New Antigen Receptor Ancestral

Ginglymostoma cirratum

UniProt Q8JGG7

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 12–95 Fragment:variable domain Lysozyme C × 1 (P00698) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain O; UniProt 12–95 Fragment:variable domain Lysozyme C × 1 (P00698) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 12–95 Fragment:variable domain Lysozyme C × 1 (P00698) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q8JGG7_GINCI
Isoform
PDB entities 1
Chains and sequence ranges Author chain N; PDBConstruct 1–84; UniProt 12–95 Author chain O; PDBConstruct 1–84; UniProt 12–95 Author chain P; PDBConstruct 1–84; UniProt 12–95

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 Ancestral × 1 (Q8JGG7) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291
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 Ancestral × 1 (Q8JGG7) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain Q; UniProt 19–147 Not recorded New Antigen Receptor Ancestral × 1 (Q8JGG7) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.50 Å R-free 0.291

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 1448 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 Author chain Q; 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 2i26

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2i26
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2i26
Deposition date deposition_date2006-08-15
Structure title titleCrystal structure analysis of the nurse shark new antigen receptor ancestral 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_guinier32.65
Radius of gyration Rg (electron density) rg_electron32.18
Forward intensity I(0) i0125923000.00
Molecular weight molecular_weight81540.0 kDa
Excluded volume excluded_volume98832 ų
Envelope volume envelope_volume131880 ų
Hydration-shell volume shell_volume36053 ų
Envelope diameter envelope_diameter111.3
Shell Rg shell_rg37.33
Envelope Rg envelope_rg31.50
Shape Rg shape_rg32.11
Total Rg total_rg32.76
Total atoms total_atoms5698
Residues n_residues736
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 dmax108.5
Rg (real space) rg_real32.70
Rg uncertainty (real space) rg_real_error1.14
I(0) (real space) i0_real1.2590e+08
I(0) uncertainty (real space) i0_real_error2.1210e+06
Rg (reciprocal space) rg_reciprocal32.68
I(0) (reciprocal space) i0_reciprocal125900000.0000
Solution quality estimate total_estimate0.8881
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.8
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10990000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.929

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd2i26l_
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_idd2i26m_
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_idd2i26n1
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_idd2i26n2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i26o2
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_idd2i26o3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i26p2
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_idd2i26p3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i26q_
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

CATH v4.4 (6 domains)

Domain ID domain_id2i26L00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id2i26M00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id2i26N00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i26O00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i26P00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i26Q00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)