6mow

Crystal Structure of the apo R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121Q mutant of Human Cellular Retinoic Acid Binding Protein II at 2.3 Angstrom Resolution

Method: X-RAY DIFFRACTION Dmax: 49.3 Å Quality: REASONABLE

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 Fragment:R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121Q No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;PEG3350, Sodium Malonate Resolution 2.35 Å R-free 0.259
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–138 Fragment:R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121Q No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;PEG3350, Sodium Malonate Resolution 2.35 Å R-free 0.259

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

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 6mow

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6mow
Deposition date deposition_date2018-10-04
Structure title titleCrystal Structure of the apo R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121Q mutant of Human Cellular Retinoic Acid Binding Protein II at 2.3 Angstrom Resolution
Keywords keywordsiLBP, Rhodopsin mimic, 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_guinier15.78
Radius of gyration Rg (electron density) rg_electron14.57
Forward intensity I(0) i04642270.00
Molecular weight molecular_weight15560.0 kDa
Excluded volume excluded_volume19578 ų
Envelope volume envelope_volume22540 ų
Hydration-shell volume shell_volume13137 ų
Envelope diameter envelope_diameter48.2
Shell Rg shell_rg20.37
Envelope Rg envelope_rg14.76
Shape Rg shape_rg14.53
Total Rg total_rg15.83
Total atoms total_atoms1092
Residues n_residues137
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 dmax49.3
Rg (real space) rg_real15.67
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real4.6420e+06
I(0) uncertainty (real space) i0_real_error4.7090e+04
Rg (reciprocal space) rg_reciprocal15.68
I(0) (reciprocal space) i0_reciprocal4642000.0000
Solution quality estimate total_estimate0.7223
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.6
Skewness Skewness skewness0.117
Kurtosis Kurtosis kurtosis-0.366
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha817700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.991; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6mowa_
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 (1 domains)

Domain ID domain_id6mowA00
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)