1ic7

CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX

Method: X-RAY DIFFRACTION Dmax: 71.1 Å Quality: EXCELLENT

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

LYSOZYME BINDING IG KAPPA CHAIN

Mus musculus

UniProt P01642

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain L; UniProt 1–107 Not recorded IGG1 FAB CHAIN H × 1 (P01823) LYSOZYME C × 1 (P00698) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;HEPES, PEG6000, MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.230

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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KV5I_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain L; PDBConstruct 1–107; UniProt 1–107

IGG1 FAB CHAIN H

Mus musculus

UniProt P01823

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 1–114 Fragment:RESIDUES 1-114 Mutation:D32A/D99A LYSOZYME BINDING IG KAPPA CHAIN × 1 (P01642) LYSOZYME C × 1 (P00698) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;HEPES, PEG6000, MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.230

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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HV47_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain H; PDBConstruct 1–114; UniProt 1–114

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain Y; UniProt 19–147 Not recorded LYSOZYME BINDING IG KAPPA CHAIN × 1 (P01642) IGG1 FAB CHAIN H × 1 (P01823) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;HEPES, PEG6000, MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.230

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 3
Chains and sequence ranges Author chain Y; 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 1ic7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ic7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ic7
Deposition date deposition_date2001-03-30
Structure title titleCRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX
Keywords keywordsantigen-antibody complex, HYHEL-10, ANTI-HEN EGG WHITE LYSOZYME ANTIBODY, PROTEIN BINDING-HYDROLASE COMPLEX; PROTEIN BINDING/HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.03
Radius of gyration Rg (electron density) rg_electron21.07
Forward intensity I(0) i027745300.00
Molecular weight molecular_weight38635.0 kDa
Excluded volume excluded_volume47586 ų
Envelope volume envelope_volume55612 ų
Hydration-shell volume shell_volume22320 ų
Envelope diameter envelope_diameter73.0
Shell Rg shell_rg27.60
Envelope Rg envelope_rg21.23
Shape Rg shape_rg21.00
Total Rg total_rg22.05
Total atoms total_atoms2715
Residues n_residues350
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 dmax71.1
Rg (real space) rg_real21.93
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real2.7750e+07
I(0) uncertainty (real space) i0_real_error3.4770e+05
Rg (reciprocal space) rg_reciprocal21.95
I(0) (reciprocal space) i0_reciprocal27750000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha5374000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1ic7h_
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_idd1ic7l_
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_idd1ic7y_
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 (3 domains)

Domain ID domain_id1ic7H00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ic7L00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ic7Y00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)