4phi

Crystal structure of HEWL with hexatungstotellurate(VI)

Method: X-RAY DIFFRACTION Dmax: 85.8 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–147 Not recorded TEW 6-tungstotellurate(VI) × 2 NA SODIUM ION × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;293 K;1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8 Resolution 1.81 Å R-free 0.200
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–147 Chain B; UniProt 19–147 Chain C; UniProt 19–147 Chain D; UniProt 19–147 Not recorded TEW 6-tungstotellurate(VI) × 8 NA SODIUM ION × 6 GOL GLYCEROL × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;293 K;1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8 Resolution 1.81 Å R-free 0.200
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 19–147 Not recorded TEW 6-tungstotellurate(VI) × 5 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;293 K;1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8 Resolution 1.81 Å R-free 0.200
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 19–147 Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;293 K;1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8 Resolution 1.81 Å R-free 0.200
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 19–147 Not recorded TEW 6-tungstotellurate(VI) × 1 NA SODIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;293 K;1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8 Resolution 1.81 Å R-free 0.200

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 1446 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 19–147 Author chain B; PDBConstruct 1–129; UniProt 19–147 Author chain C; PDBConstruct 1–129; UniProt 19–147 Author chain D; 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 4phi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4phi
Deposition date deposition_date2014-05-06
Structure title titleCrystal structure of HEWL with hexatungstotellurate(VI)
Keywords keywordspolyoxometalate, Anderson Evans type, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.61
Radius of gyration Rg (electron density) rg_electron25.33
Forward intensity I(0) i0139549000.00
Molecular weight molecular_weight68583.0 kDa
Excluded volume excluded_volume72114 ų
Envelope volume envelope_volume87155 ų
Hydration-shell volume shell_volume29252 ų
Envelope diameter envelope_diameter88.8
Shell Rg shell_rg31.87
Envelope Rg envelope_rg24.76
Shape Rg shape_rg24.79
Total Rg total_rg26.83
Total atoms total_atoms7793
Residues n_residues508
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 dmax85.8
Rg (real space) rg_real26.52
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real1.3950e+08
I(0) uncertainty (real space) i0_real_error1.9870e+06
Rg (reciprocal space) rg_reciprocal26.55
I(0) (reciprocal space) i0_reciprocal139600000.0000
Solution quality estimate total_estimate0.8816
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.5
Skewness Skewness skewness0.204
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1302000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4phia_
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
Domain ID domain_idd4phib_
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
Domain ID domain_idd4phic_
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
Domain ID domain_idd4phid_
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 (4 domains)

Domain ID domain_id4phiA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4phiB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4phiC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4phiD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)