4m7m

Crystal structure of the R111K:R132Q:Y134F:T54V:R59W:A32W mutant of the Cellular Retinoic Acid Binding Protein Type II in complex with All-Trans Retinal at 2.57 Angstrom Resolution

Method: X-RAY DIFFRACTION Dmax: 49.5 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:R132Q:Y134F:T54V:R59W:A32W RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;0.1 M malonate, pH 7.0, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.57 Å R-free 0.253

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 138 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 4m7m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4m7m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4m7m
Deposition date deposition_date2013-08-12
Structure title titleCrystal structure of the R111K:R132Q:Y134F:T54V:R59W:A32W mutant of the Cellular Retinoic Acid Binding Protein Type II in complex with All-Trans Retinal at 2.57 Angstrom Resolution
Keywords keywordsprotein engineering, wavelength regulation, pH-sensing, Retinylidene PSB, Iminium, 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_guinier15.73
Radius of gyration Rg (electron density) rg_electron14.37
Forward intensity I(0) i04350420.00
Molecular weight molecular_weight15370.0 kDa
Excluded volume excluded_volume19463 ų
Envelope volume envelope_volume21869 ų
Hydration-shell volume shell_volume12960 ų
Envelope diameter envelope_diameter49.8
Shell Rg shell_rg20.10
Envelope Rg envelope_rg14.54
Shape Rg shape_rg14.35
Total Rg total_rg15.63
Total atoms total_atoms1082
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 dmax49.5
Rg (real space) rg_real15.61
Rg uncertainty (real space) rg_real_error0.20
I(0) (real space) i0_real4.3500e+06
I(0) uncertainty (real space) i0_real_error4.0550e+04
Rg (reciprocal space) rg_reciprocal15.63
I(0) (reciprocal space) i0_reciprocal4350000.0000
Solution quality estimate total_estimate0.8898
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7
Skewness Skewness skewness0.083
Kurtosis Kurtosis kurtosis-0.375
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha709000.0000
Real-space data points n_real_points80
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: 0.990; Smooth: 0.969

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4m7ma_
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_id4m7mA00
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)