4ykm

Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 71.5 Å Quality: GOOD

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

Cellular retinoic acid-binding protein 2

Homo sapiens

UniProt P29373

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 A; UniProt 2–138 Mutation:R111K, Y134F, T54V, R132Q, P39Q, R59Y, A32W, F3Q RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;20% PEG3350, 0.1M Bis Tris Propane pH=6.0, 0.2M Sodium Floride Resolution 1.58 Å R-free 0.216
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–138 Mutation:R111K, Y134F, T54V, R132Q, P39Q, R59Y, A32W, F3Q RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;20% PEG3350, 0.1M Bis Tris Propane pH=6.0, 0.2M Sodium Floride Resolution 1.58 Å R-free 0.216

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.

84 other PDB entries and 137 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RABP2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–137; UniProt 2–138 Author chain B; PDBConstruct 1–137; UniProt 2–138

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 4ykm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ykm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ykm
Deposition date deposition_date2015-03-04
Structure title titleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution
Keywords keywordsPhotoswitchable protein, Rhodopsin mimic, Retinal isomerization, Retinal iminium pKa change, Protein engineering, 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_guinier21.63
Radius of gyration Rg (electron density) rg_electron20.65
Forward intensity I(0) i016625300.00
Molecular weight molecular_weight31773.0 kDa
Excluded volume excluded_volume40242 ų
Envelope volume envelope_volume47659 ų
Hydration-shell volume shell_volume19820 ų
Envelope diameter envelope_diameter71.8
Shell Rg shell_rg26.48
Envelope Rg envelope_rg20.77
Shape Rg shape_rg20.66
Total Rg total_rg21.47
Total atoms total_atoms2232
Residues n_residues274
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 dmax71.5
Rg (real space) rg_real21.65
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real1.6630e+07
I(0) uncertainty (real space) i0_real_error2.1020e+05
Rg (reciprocal space) rg_reciprocal21.64
I(0) (reciprocal space) i0_reciprocal16630000.0000
Solution quality estimate total_estimate0.8812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3806000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ykma_
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_idd4ykmb_
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 (2 domains)

Domain ID domain_id4ykmA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id4ykmB00
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)