3kza

Crystal structure of Gyuba, a patched chimera of b-lactglobulin

Method: X-RAY DIFFRACTION Dmax: 76.4 Å Quality: GOOD

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

Beta-lactoglobulin

Equus caballus

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 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 96–102 Chain A; UniProt 105–111 Chain A; UniProt 118–124 Chain A; UniProt 133–140 Chain A; UniProt 146–154 Chain A; UniProt 33–43 Chain A; UniProt 161–169 Chain A; UniProt 58–65 Chain A; UniProt 68–78 Chain A; UniProt 82–89 Chain B; UniProt 96–102 Chain B; UniProt 105–111 Chain B; UniProt 118–124 Chain B; UniProt 133–140 Chain B; UniProt 146–154 Chain B; UniProt 33–43 Chain B; UniProt 161–169 Chain B; UniProt 58–65 Chain B; UniProt 68–78 Chain B; UniProt 82–89 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 96–102 Chain A; UniProt 105–111 Chain A; UniProt 118–124 Chain A; UniProt 133–140 Chain A; UniProt 146–154 Chain A; UniProt 33–43 Chain A; UniProt 161–169 Chain A; UniProt 58–65 Chain A; UniProt 68–78 Chain A; UniProt 82–89 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 96–102 Chain B; UniProt 105–111 Chain B; UniProt 118–124 Chain B; UniProt 133–140 Chain B; UniProt 146–154 Chain B; UniProt 33–43 Chain B; UniProt 161–169 Chain B; UniProt 58–65 Chain B; UniProt 68–78 Chain B; UniProt 82–89 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285

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 80–86; UniProt 96–102 Author chain A; PDBConstruct 89–95; UniProt 105–111 Author chain A; PDBConstruct 102–108; UniProt 118–124 Author chain A; PDBConstruct 117–124; UniProt 133–140 Author chain A; PDBConstruct 130–138; UniProt 146–154 Author chain A; PDBConstruct 17–27; UniProt 33–43 Author chain A; PDBConstruct 145–153; UniProt 161–169 Author chain A; PDBConstruct 42–49; UniProt 58–65 Author chain A; PDBConstruct 52–62; UniProt 68–78 Author chain A; PDBConstruct 66–73; UniProt 82–89 Author chain B; PDBConstruct 80–86; UniProt 96–102 Author chain B; PDBConstruct 89–95; UniProt 105–111 Author chain B; PDBConstruct 102–108; UniProt 118–124 Author chain B; PDBConstruct 117–124; UniProt 133–140 Author chain B; PDBConstruct 130–138; UniProt 146–154 Author chain B; PDBConstruct 17–27; UniProt 33–43 Author chain B; PDBConstruct 145–153; UniProt 161–169 Author chain B; PDBConstruct 42–49; UniProt 58–65 Author chain B; PDBConstruct 52–62; UniProt 68–78 Author chain B; PDBConstruct 66–73; UniProt 82–89

Beta-lactoglobulin

Equus caballus

UniProt P02758

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–34 Chain A; UniProt 105–106 Chain A; UniProt 114–119 Chain A; UniProt 127–134 Chain A; UniProt 143–147 Chain A; UniProt 156–161 Chain A; UniProt 172–180 Chain A; UniProt 46–59 Chain A; UniProt 68–69 Chain A; UniProt 81–83 Chain A; UniProt 92–97 Chain B; UniProt 19–34 Chain B; UniProt 105–106 Chain B; UniProt 114–119 Chain B; UniProt 127–134 Chain B; UniProt 143–147 Chain B; UniProt 156–161 Chain B; UniProt 172–180 Chain B; UniProt 46–59 Chain B; UniProt 68–69 Chain B; UniProt 81–83 Chain B; UniProt 92–97 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–34 Chain A; UniProt 105–106 Chain A; UniProt 114–119 Chain A; UniProt 127–134 Chain A; UniProt 143–147 Chain A; UniProt 156–161 Chain A; UniProt 172–180 Chain A; UniProt 46–59 Chain A; UniProt 68–69 Chain A; UniProt 81–83 Chain A; UniProt 92–97 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 19–34 Chain B; UniProt 105–106 Chain B; UniProt 114–119 Chain B; UniProt 127–134 Chain B; UniProt 143–147 Chain B; UniProt 156–161 Chain B; UniProt 172–180 Chain B; UniProt 46–59 Chain B; UniProt 68–69 Chain B; UniProt 81–83 Chain B; UniProt 92–97 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.285

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name LACB1_HORSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–16; UniProt 19–34 Author chain A; PDBConstruct 87–88; UniProt 105–106 Author chain A; PDBConstruct 96–101; UniProt 114–119 Author chain A; PDBConstruct 109–116; UniProt 127–134 Author chain A; PDBConstruct 125–129; UniProt 143–147 Author chain A; PDBConstruct 139–144; UniProt 156–161 Author chain A; PDBConstruct 154–162; UniProt 172–180 Author chain A; PDBConstruct 28–41; UniProt 46–59 Author chain A; PDBConstruct 50–51; UniProt 68–69 Author chain A; PDBConstruct 63–65; UniProt 81–83 Author chain A; PDBConstruct 74–79; UniProt 92–97 Author chain B; PDBConstruct 1–16; UniProt 19–34 Author chain B; PDBConstruct 87–88; UniProt 105–106 Author chain B; PDBConstruct 96–101; UniProt 114–119 Author chain B; PDBConstruct 109–116; UniProt 127–134 Author chain B; PDBConstruct 125–129; UniProt 143–147 Author chain B; PDBConstruct 139–144; UniProt 156–161 Author chain B; PDBConstruct 154–162; UniProt 172–180 Author chain B; PDBConstruct 28–41; UniProt 46–59 Author chain B; PDBConstruct 50–51; UniProt 68–69 Author chain B; PDBConstruct 63–65; UniProt 81–83 Author chain B; PDBConstruct 74–79; UniProt 92–97

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 3kza

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3kza
Deposition date deposition_date2009-12-08
Structure title titleCrystal structure of Gyuba, a patched chimera of b-lactglobulin
Keywords keywordsartificial protein, chimera protein, Disulfide bond, Milk protein, Retinol-binding, Secreted, Transport, 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_guinier22.03
Radius of gyration Rg (electron density) rg_electron21.30
Forward intensity I(0) i018782800.00
Molecular weight molecular_weight33348.0 kDa
Excluded volume excluded_volume42002 ų
Envelope volume envelope_volume49865 ų
Hydration-shell volume shell_volume20338 ų
Envelope diameter envelope_diameter78.5
Shell Rg shell_rg27.10
Envelope Rg envelope_rg21.47
Shape Rg shape_rg21.32
Total Rg total_rg22.05
Total atoms total_atoms2336
Residues n_residues298
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 dmax76.4
Rg (real space) rg_real22.14
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real1.8780e+07
I(0) uncertainty (real space) i0_real_error2.5430e+05
Rg (reciprocal space) rg_reciprocal22.12
I(0) (reciprocal space) i0_reciprocal18780000.0000
Solution quality estimate total_estimate0.7611
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9
Skewness Skewness skewness0.515
Kurtosis Kurtosis kurtosis-0.158
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13330000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3kzaa_
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_idd3kzab_
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_id3kzaA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id3kzaB00
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)