5lsh

human lysozyme in complex with a tetrasaccharide fragment of the O-chain of LPS from Klebsiella pneumoniae

Method: X-RAY DIFFRACTION Dmax: 57.2 Å Quality: REASONABLE

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

Lysozyme C

Homo sapiens

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 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–148 Not recorded alpha-D-galactopyranose-(1-3)-beta-D-galactofuranose-(1-3)-alpha-D-galactopyranose-(1-3)-propyl beta-D-galactofuranoside × 1 CL CHLORIDE ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.8 M NaCl, 25 mM NaOAc, pH 5.4 Resolution 1.06 Å R-free 0.203

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 1–130; UniProt 19–148

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 5lsh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lsh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lsh
Deposition date deposition_date2016-08-26
Structure title titlehuman lysozyme in complex with a tetrasaccharide fragment of the O-chain of LPS from Klebsiella pneumoniae
Keywords keywordslectin, complex, LPS, O-chain, sugar binding protein; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.37
Radius of gyration Rg (electron density) rg_electron14.09
Forward intensity I(0) i05335610.00
Molecular weight molecular_weight15550.0 kDa
Excluded volume excluded_volume18977 ų
Envelope volume envelope_volume20774 ų
Hydration-shell volume shell_volume12519 ų
Envelope diameter envelope_diameter51.4
Shell Rg shell_rg19.92
Envelope Rg envelope_rg14.43
Shape Rg shape_rg14.05
Total Rg total_rg15.24
Total atoms total_atoms1081
Residues n_residues130
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 dmax57.2
Rg (real space) rg_real15.28
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real5.3360e+06
I(0) uncertainty (real space) i0_real_error6.1880e+04
Rg (reciprocal space) rg_reciprocal15.29
I(0) (reciprocal space) i0_reciprocal5336000.0000
Solution quality estimate total_estimate0.7444
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.306
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1167000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.580; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5lsha_
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_id5lshA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)