6wp0

The Crystal Structure of Domain-Swapped Trimer Q108K:T51D variant of HCRBPII

Method: X-RAY DIFFRACTION Dmax: 142.6 Å Quality: GOOD

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

Retinol-binding protein 2

Homo sapiens

UniProt P50120

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 2–134 Chain I; UniProt 2–134 Chain K; UniProt 2–134 Mutation:Q108K, T51D GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;sodium acetate, ammonium acetate, PEG 4000 Resolution 2.78 Å R-free 0.321
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 2–134 Chain J; UniProt 2–134 Chain L; UniProt 2–134 Mutation:Q108K, T51D GOL GLYCEROL × 10 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;sodium acetate, ammonium acetate, PEG 4000 Resolution 2.78 Å R-free 0.321
3 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 2–134 Chain E; UniProt 2–134 Chain G; UniProt 2–134 Mutation:Q108K, T51D GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;sodium acetate, ammonium acetate, PEG 4000 Resolution 2.78 Å R-free 0.321
4 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 2–134 Chain F; UniProt 2–134 Chain H; UniProt 2–134 Mutation:Q108K, T51D GOL GLYCEROL × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;sodium acetate, ammonium acetate, PEG 4000 Resolution 2.78 Å R-free 0.321

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 197 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RET2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–133; UniProt 2–134 Author chain B; PDBConstruct 1–133; UniProt 2–134 Author chain C; PDBConstruct 1–133; UniProt 2–134 Author chain D; PDBConstruct 1–133; UniProt 2–134 Author chain E; PDBConstruct 1–133; UniProt 2–134 Author chain F; PDBConstruct 1–133; UniProt 2–134 Author chain G; PDBConstruct 1–133; UniProt 2–134 Author chain H; PDBConstruct 1–133; UniProt 2–134 Author chain I; PDBConstruct 1–133; UniProt 2–134 Author chain J; PDBConstruct 1–133; UniProt 2–134 Author chain K; PDBConstruct 1–133; UniProt 2–134 Author chain L; PDBConstruct 1–133; UniProt 2–134

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 6wp0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wp0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wp0
Deposition date deposition_date2020-04-26
Structure title titleThe Crystal Structure of Domain-Swapped Trimer Q108K:T51D variant of HCRBPII
Keywords keywordsiLBP, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.92
Radius of gyration Rg (electron density) rg_electron42.49
Forward intensity I(0) i0526120000.00
Molecular weight molecular_weight182380.0 kDa
Excluded volume excluded_volume225820 ų
Envelope volume envelope_volume331650 ų
Hydration-shell volume shell_volume66155 ų
Envelope diameter envelope_diameter150.1
Shell Rg shell_rg46.93
Envelope Rg envelope_rg41.34
Shape Rg shape_rg42.50
Total Rg total_rg42.70
Total atoms total_atoms12836
Residues n_residues1596
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 dmax142.6
Rg (real space) rg_real42.83
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real5.2610e+08
I(0) uncertainty (real space) i0_real_error8.4160e+06
Rg (reciprocal space) rg_reciprocal42.92
I(0) (reciprocal space) i0_reciprocal526200000.0000
Solution quality estimate total_estimate0.8830
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.1
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.300
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35350000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.875

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd6wp0a_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0b_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0c_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0d_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0e_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0f_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0g_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0h_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0i_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0j_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0k_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like
Domain ID domain_idd6wp0l_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like

8. Citations (2)

9. Files and Curves (10)