6c7z

Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with synthetic Ligand Julolidine

Method: X-RAY DIFFRACTION Dmax: 72.2 Å Quality: GOOD

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–134 Mutation:Q108K,K40L,T51V,R58F ACT ACETATE ION × 1 JLO (2E,4E)-3-methyl-5-(2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-9-yl)penta-2,4-dienal × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298 K;30% PEG 4000, 0.1M Ammonium Acetate, 0.1 M Sodium Acetate pH=4.5 Resolution 1.42 Å R-free 0.256
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–134 Mutation:Q108K,K40L,T51V,R58F ACT ACETATE ION × 1 JLO (2E,4E)-3-methyl-5-(2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-9-yl)penta-2,4-dienal × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298 K;30% PEG 4000, 0.1M Ammonium Acetate, 0.1 M Sodium Acetate pH=4.5 Resolution 1.42 Å R-free 0.256

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

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 6c7z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c7z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c7z
Deposition date deposition_date2018-01-23
Structure title titleCrystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with synthetic Ligand Julolidine
Keywords keywordsProtein Engineering, Ratiometric pH probe, hCRBPII, 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_guinier21.84
Radius of gyration Rg (electron density) rg_electron20.95
Forward intensity I(0) i017405900.00
Molecular weight molecular_weight31678.0 kDa
Excluded volume excluded_volume39683 ų
Envelope volume envelope_volume46227 ų
Hydration-shell volume shell_volume19257 ų
Envelope diameter envelope_diameter72.4
Shell Rg shell_rg26.29
Envelope Rg envelope_rg21.05
Shape Rg shape_rg20.97
Total Rg total_rg21.65
Total atoms total_atoms2234
Residues n_residues266
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 dmax72.2
Rg (real space) rg_real21.91
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real1.7410e+07
I(0) uncertainty (real space) i0_real_error2.5190e+05
Rg (reciprocal space) rg_reciprocal21.90
I(0) (reciprocal space) i0_reciprocal17410000.0000
Solution quality estimate total_estimate0.8769
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4155000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6c7za_
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_idd6c7zb_
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_id6c7zA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6c7zB00
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)