2zwb

Neutron crystal structure of wild type human lysozyme in D2O

Method: NEUTRON DIFFRACTION Dmax: 51.8 Å Quality: GOOD

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–148 Not recorded No other associated polymer NEUTRON DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 4.3;293 K;PH 4.30(PD), SMALL TUBES, temperature 293K Resolution 1.80 Å R-free 0.247

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 2zwb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2zwb
Deposition date deposition_date2008-12-02
Structure title titleNeutron crystal structure of wild type human lysozyme in D2O
Keywords keywordsNEUTRON D2O HYDROGEN HYDRATION, HYDROLASE, Amyloid, Amyloidosis, Antimicrobial, Bacteriolytic enzyme, Disease mutation, Glycosidase; HYDROLASE
Experimental Method methodNEUTRON DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.82
Radius of gyration Rg (electron density) rg_electron14.33
Forward intensity I(0) i05002800.00
Molecular weight molecular_weight16488.0 kDa
Excluded volume excluded_volume20608 ų
Envelope volume envelope_volume23417 ų
Hydration-shell volume shell_volume13502 ų
Envelope diameter envelope_diameter52.1
Shell Rg shell_rg20.55
Envelope Rg envelope_rg14.95
Shape Rg shape_rg14.57
Total Rg total_rg14.87
Total atoms total_atoms2183
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 dmax51.8
Rg (real space) rg_real15.73
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real5.0030e+06
I(0) uncertainty (real space) i0_real_error6.2010e+04
Rg (reciprocal space) rg_reciprocal15.74
I(0) (reciprocal space) i0_reciprocal5003000.0000
Solution quality estimate total_estimate0.8030
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.5
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1115000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2zwba_
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_id2zwbA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)