2gj5

Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin

Method: X-RAY DIFFRACTION Dmax: 50.0 Å Quality: GOOD

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

Beta-lactoglobulin

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 17–178 Not recorded VD3 (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M HEPES, 1.4M tri-sodium citrate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.298

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

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 2gj5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gj5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gj5
Deposition date deposition_date2006-03-30
Structure title titleCrystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin
Keywords keywordsbeta-lactoglobulin, vitamin D3, 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_guinier16.28
Radius of gyration Rg (electron density) rg_electron14.87
Forward intensity I(0) i05930910.00
Molecular weight molecular_weight18929.0 kDa
Excluded volume excluded_volume24327 ų
Envelope volume envelope_volume26600 ų
Hydration-shell volume shell_volume14782 ų
Envelope diameter envelope_diameter48.7
Shell Rg shell_rg21.17
Envelope Rg envelope_rg15.18
Shape Rg shape_rg14.88
Total Rg total_rg16.11
Total atoms total_atoms1328
Residues n_residues161
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 dmax50.0
Rg (real space) rg_real16.13
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real5.9310e+06
I(0) uncertainty (real space) i0_real_error6.3970e+04
Rg (reciprocal space) rg_reciprocal16.14
I(0) (reciprocal space) i0_reciprocal5931000.0000
Solution quality estimate total_estimate0.8921
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.4
Skewness Skewness skewness-0.004
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.4900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1279000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2gj5a_
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 (1 domains)

Domain ID domain_id2gj5A00
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)