3nq9

Bovine beta-lactoglobulin complex with caprylic acid

Method: X-RAY DIFFRACTION Dmax: 51.4 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 OCA OCTANOIC ACID (CAPRYLIC ACID) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;1.34M trisodium citrate, 0.1M Tris-HCl buffer, 10mM caprylic acid in 96% ethanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.90 Å R-free 0.309

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 3nq9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3nq9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3nq9
Deposition date deposition_date2010-06-29
Structure title titleBovine beta-lactoglobulin complex with caprylic acid
Keywords keywordsbeta-lactoglobulin, lipocalin, bovine milk, caprylic acid, octanoic acid, fatty acid, 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_guinier16.32
Radius of gyration Rg (electron density) rg_electron14.89
Forward intensity I(0) i06105830.00
Molecular weight molecular_weight18453.0 kDa
Excluded volume excluded_volume23391 ų
Envelope volume envelope_volume26445 ų
Hydration-shell volume shell_volume14710 ų
Envelope diameter envelope_diameter49.6
Shell Rg shell_rg21.11
Envelope Rg envelope_rg15.19
Shape Rg shape_rg14.89
Total Rg total_rg16.07
Total atoms total_atoms1291
Residues n_residues162
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 dmax51.4
Rg (real space) rg_real16.16
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real6.1060e+06
I(0) uncertainty (real space) i0_real_error7.0560e+04
Rg (reciprocal space) rg_reciprocal16.18
I(0) (reciprocal space) i0_reciprocal6106000.0000
Solution quality estimate total_estimate0.8856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1
Skewness Skewness skewness-0.002
Kurtosis Kurtosis kurtosis-0.483
Angular range angular_range— – 0.4900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1462000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3nq9a_
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_id3nq9A00
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)