3d96

Crystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution

Method: X-RAY DIFFRACTION Dmax: 75.5 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:R132K, Y134F No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;30% (W/V) PEG 4000, 0.1 M TRIS-HCL, 0.2 M SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.71 Å R-free 0.222
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–138 Mutation:R132K, Y134F ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;30% (W/V) PEG 4000, 0.1 M TRIS-HCL, 0.2 M SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.71 Å R-free 0.222

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 3d96

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3d96
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3d96
Deposition date deposition_date2008-05-26
Structure title titleCrystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution
Keywords keywords;CRABPII, RETINOIC ACID, RETINOIDS, BETA BARREL, HIGH RESOLUTION, MUTANT, Nucleus, Retinol-binding, Transport, Vitamin A, 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_guinier22.84
Radius of gyration Rg (electron density) rg_electron22.17
Forward intensity I(0) i015885200.00
Molecular weight molecular_weight30204.0 kDa
Excluded volume excluded_volume37876 ų
Envelope volume envelope_volume48456 ų
Hydration-shell volume shell_volume18972 ų
Envelope diameter envelope_diameter75.9
Shell Rg shell_rg27.75
Envelope Rg envelope_rg21.70
Shape Rg shape_rg22.18
Total Rg total_rg22.90
Total atoms total_atoms2121
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 dmax75.5
Rg (real space) rg_real22.87
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real1.5890e+07
I(0) uncertainty (real space) i0_real_error2.0850e+05
Rg (reciprocal space) rg_reciprocal22.86
I(0) (reciprocal space) i0_reciprocal15890000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9
Skewness Skewness skewness0.327
Kurtosis Kurtosis kurtosis-0.511
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3354000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.988

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_idd3d96a_
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_idd3d96b_
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_id3d96A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id3d96B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain

8. Citations (2)

9. Files and Curves (10)