2akq

The structure of bovine B-lactoglobulin A in crystals grown at very low ionic strength

Method: X-RAY DIFFRACTION Dmax: 102.2 Å Quality: GOOD

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

Beta-lactoglobulin variant A

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 17–178 Chain B; UniProt 17–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 5.2;295 K;Ultra pure water, pH 5.20, MICRODIALYSIS, temperature 295K Resolution 3.00 Å R-free 0.266
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 17–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 5.2;295 K;Ultra pure water, pH 5.20, MICRODIALYSIS, temperature 295K Resolution 3.00 Å R-free 0.266
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 17–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 5.2;295 K;Ultra pure water, pH 5.20, MICRODIALYSIS, temperature 295K Resolution 3.00 Å R-free 0.266

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 121 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 Author chain C; PDBConstruct 1–162; UniProt 17–178 Author chain D; 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 2akq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2akq
Deposition date deposition_date2005-08-03
Structure title titleThe structure of bovine B-lactoglobulin A in crystals grown at very low ionic strength
Keywords keywordsB-lactoglbulin, crystal lattice, low ionic strength, pseudo-merohedral twinning, 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_guinier33.78
Radius of gyration Rg (electron density) rg_electron33.18
Forward intensity I(0) i075458400.00
Molecular weight molecular_weight70586.0 kDa
Excluded volume excluded_volume89176 ų
Envelope volume envelope_volume118820 ų
Hydration-shell volume shell_volume31892 ų
Envelope diameter envelope_diameter108.3
Shell Rg shell_rg37.63
Envelope Rg envelope_rg32.46
Shape Rg shape_rg33.20
Total Rg total_rg33.48
Total atoms total_atoms4943
Residues n_residues624
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 dmax102.2
Rg (real space) rg_real33.75
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real7.5460e+07
I(0) uncertainty (real space) i0_real_error1.2880e+06
Rg (reciprocal space) rg_reciprocal33.77
I(0) (reciprocal space) i0_reciprocal75460000.0000
Solution quality estimate total_estimate0.8843
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary50.0
Skewness Skewness skewness0.113
Kurtosis Kurtosis kurtosis-0.833
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32350000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.827

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2akqa_
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_idd2akqb_
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_idd2akqc_
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_idd2akqd_
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 (4 domains)

Domain ID domain_id2akqA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id2akqB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id2akqC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id2akqD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain

8. Citations (4)

9. Files and Curves (10)