4r0p

Ifqins, an amyloid forming segment from human lysozyme spanning residues 56-61

Method: X-RAY DIFFRACTION Dmax: 27.9 Å Quality: GOOD

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

Lysozyme C

OrganismNot specified

UniProt P61626

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 homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 74–79 Fragment:UNP RESIDUES 74-79 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;reservoir contained 0.1M Bis-Tris pH 6.5, 3.0M Sodium Chloride, vapor diffusion, hanging drop, temperature 298K Resolution 1.52 Å R-free 0.201

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.

201 other PDB entries and 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–6; UniProt 74–79

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 4r0p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4r0p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4r0p
Deposition date deposition_date2014-08-01
Structure title titleIfqins, an amyloid forming segment from human lysozyme spanning residues 56-61
Keywords keywordsamyloid-like protofibril, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier7.75
Radius of gyration Rg (electron density) rg_electron6.40
Forward intensity I(0) i026247.70
Molecular weight molecular_weight720.8 kDa
Excluded volume excluded_volume923 ų
Envelope volume envelope_volume1097 ų
Hydration-shell volume shell_volume2008 ų
Envelope diameter envelope_diameter23.6
Shell Rg shell_rg9.58
Envelope Rg envelope_rg6.82
Shape Rg shape_rg6.33
Total Rg total_rg8.32
Total atoms total_atoms51
Residues n_residues6
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 dmax27.9
Rg (real space) rg_real7.84
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real2.6250e+04
I(0) uncertainty (real space) i0_real_error2.5720e+02
Rg (reciprocal space) rg_reciprocal7.84
I(0) (reciprocal space) i0_reciprocal26250.0000
Solution quality estimate total_estimate0.8407
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary8.1
Skewness Skewness skewness0.498
Kurtosis Kurtosis kurtosis-0.138
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2232.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.561; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)