6jb5

Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II)

Method: X-RAY DIFFRACTION Dmax: 74.5 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 B; UniProt 19–147 Not recorded Nanobody D3-L11 × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293.15 K;20mM Tris-HCl pH 8.0, 100mM NaCl, 100mM LiCl, 18 % PEG 3350 Resolution 1.55 Å R-free 0.169

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 2
Chains and sequence ranges Author chain B; 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 6jb5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6jb5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6jb5
Deposition date deposition_date2019-01-25
Structure title titleCrystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II)
Keywords keywordsnanobody, hot-spot mutagenesis, thermodynamics, biomolecular recognition, IMMUNE SYSTEM, IMMUNE SYSTEM-HYDROLASE complex; IMMUNE SYSTEM/HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.87
Radius of gyration Rg (electron density) rg_electron20.27
Forward intensity I(0) i015883100.00
Molecular weight molecular_weight28197.0 kDa
Excluded volume excluded_volume34454 ų
Envelope volume envelope_volume39338 ų
Hydration-shell volume shell_volume17263 ų
Envelope diameter envelope_diameter75.9
Shell Rg shell_rg25.58
Envelope Rg envelope_rg20.52
Shape Rg shape_rg20.22
Total Rg total_rg21.12
Total atoms total_atoms1970
Residues n_residues255
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 dmax74.5
Rg (real space) rg_real20.98
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real1.5880e+07
I(0) uncertainty (real space) i0_real_error2.0720e+05
Rg (reciprocal space) rg_reciprocal20.96
I(0) (reciprocal space) i0_reciprocal15880000.0000
Solution quality estimate total_estimate0.7603
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.6
Skewness Skewness skewness0.514
Kurtosis Kurtosis kurtosis-0.159
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4352000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6jb5a_
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_idd6jb5b_
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 (1 domains)

Domain ID domain_id6jb5B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)