6ryt

Engineered beta-lactoglobulin: variant M107L

Method: X-RAY DIFFRACTION Dmax: 76.1 Å Quality: GOOD

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

Beta-lactoglobulin

Bos taurus

UniProt P02754

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 17–178 Chain B; UniProt 17–178 Mutation:L1A, I2S, M107L GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;2.60 M (NH4)2SO4 in 0.1 Tris-HCl pH 7.9 Resolution 2.10 Å R-free 0.278

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.

101 other PDB entries and 123 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LACB_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–162; UniProt 17–178 Author chain B; PDBConstruct 1–162; UniProt 17–178

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 6ryt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6ryt
Deposition date deposition_date2019-06-11
Structure title titleEngineered beta-lactoglobulin: variant M107L
Keywords keywordsLipocalin, mutation, lactoglobulin, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.96
Radius of gyration Rg (electron density) rg_electron21.45
Forward intensity I(0) i016786800.00
Molecular weight molecular_weight32268.0 kDa
Excluded volume excluded_volume41040 ų
Envelope volume envelope_volume49106 ų
Hydration-shell volume shell_volume19999 ų
Envelope diameter envelope_diameter78.4
Shell Rg shell_rg27.10
Envelope Rg envelope_rg21.62
Shape Rg shape_rg21.46
Total Rg total_rg22.24
Total atoms total_atoms2259
Residues n_residues290
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 dmax76.1
Rg (real space) rg_real22.09
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real1.6790e+07
I(0) uncertainty (real space) i0_real_error2.3220e+05
Rg (reciprocal space) rg_reciprocal22.06
I(0) (reciprocal space) i0_reciprocal16790000.0000
Solution quality estimate total_estimate0.7568
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.7
Skewness Skewness skewness0.526
Kurtosis Kurtosis kurtosis-0.142
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10820000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6ryta_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.1 — Retinol binding protein-like
Domain ID domain_idd6rytb_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.1 — Retinol binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id6rytA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6rytB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain

8. Citations (1)

9. Files and Curves (10)