6e7m

Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28C mutant of human Cellular Retinol Binding Protein II

Method: X-RAY DIFFRACTION Dmax: 89.6 Å Quality: EXCELLENT

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–134 Chain C; UniProt 2–134 Mutation:Q108K, T51D, A28C ACT ACETATE ION × 8 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;PEG 4000, ammonium acetate, sodium acetate Resolution 2.70 Å R-free 0.296
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–134 Chain D; UniProt 2–134 Mutation:Q108K, T51D, A28C ACT ACETATE ION × 2 GOL GLYCEROL × 2 RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;PEG 4000, ammonium acetate, sodium acetate Resolution 2.70 Å R-free 0.296

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 199 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

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 6e7m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6e7m
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6e7m
Deposition date deposition_date2018-07-26
Structure title titleCrystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28C mutant of human Cellular Retinol Binding Protein II
Keywords keywordsRetinol, iLBP, Protein Switch, 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_guinier29.16
Radius of gyration Rg (electron density) rg_electron28.23
Forward intensity I(0) i069029100.00
Molecular weight molecular_weight63774.0 kDa
Excluded volume excluded_volume79221 ų
Envelope volume envelope_volume102090 ų
Hydration-shell volume shell_volume30370 ų
Envelope diameter envelope_diameter89.0
Shell Rg shell_rg35.36
Envelope Rg envelope_rg27.76
Shape Rg shape_rg28.25
Total Rg total_rg28.89
Total atoms total_atoms4481
Residues n_residues532
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 dmax89.6
Rg (real space) rg_real29.06
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real6.9030e+07
I(0) uncertainty (real space) i0_real_error9.2000e+05
Rg (reciprocal space) rg_reciprocal29.10
I(0) (reciprocal space) i0_reciprocal69030000.0000
Solution quality estimate total_estimate0.9091
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.1
Skewness Skewness skewness0.103
Kurtosis Kurtosis kurtosis-0.668
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22740000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6e7ma_
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_idd6e7mb_
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_idd6e7mc_
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_idd6e7md_
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

CATH v4.4 (4 domains)

Domain ID domain_id6e7mA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6e7mB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6e7mC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6e7mD00
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)