6nkq

The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8

Method: X-RAY DIFFRACTION Dmax: 99.9 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 B; UniProt 1–178 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 1–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 1–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–178 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3.8;293 K;Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours Resolution 2.30 Å R-free 0.261

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 118 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 1–178; UniProt 1–178 Author chain B; PDBConstruct 1–178; UniProt 1–178 Author chain C; PDBConstruct 1–178; UniProt 1–178 Author chain D; PDBConstruct 1–178; UniProt 1–178 Author chain E; PDBConstruct 1–178; UniProt 1–178 Author chain F; PDBConstruct 1–178; UniProt 1–178

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 6nkq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6nkq
Deposition date deposition_date2019-01-07
Structure title titleThe structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8
Keywords keywordsmilk, twinning, space group, whey protein, molecular replacement, Tanford transition, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.96
Radius of gyration Rg (electron density) rg_electron30.35
Forward intensity I(0) i0174397000.00
Molecular weight molecular_weight107370.0 kDa
Excluded volume excluded_volume135570 ų
Envelope volume envelope_volume167950 ų
Hydration-shell volume shell_volume45288 ų
Envelope diameter envelope_diameter109.5
Shell Rg shell_rg38.11
Envelope Rg envelope_rg30.14
Shape Rg shape_rg30.34
Total Rg total_rg31.07
Total atoms total_atoms7519
Residues n_residues954
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 dmax99.9
Rg (real space) rg_real30.82
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real1.7440e+08
I(0) uncertainty (real space) i0_real_error2.6280e+06
Rg (reciprocal space) rg_reciprocal30.88
I(0) (reciprocal space) i0_reciprocal174400000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.1
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha114400000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6nkqa_
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_idd6nkqb_
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_idd6nkqc_
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_idd6nkqd_
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_idd6nkqe_
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_idd6nkqf_
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 (6 domains)

Domain ID domain_id6nkqA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6nkqB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6nkqC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6nkqD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6nkqE00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6nkqF00
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)