7lhm

Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A:Q38L mutant of cellular retinol binding protein II complex with all-trans-retinal

Method: X-RAY DIFFRACTION Dmax: 71.9 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,T53C,R58W,T29L,Y19W,Q4A,Q38L ACT ACETATE ION × 1 RET RETINAL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K Resolution 1.50 Å R-free 0.222
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–134 Mutation:Q108K,K40L,T51V,T53C,R58W,T29L,Y19W,Q4A,Q38L ACT ACETATE ION × 1 RET RETINAL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K Resolution 1.50 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.

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 7lhm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lhm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7lhm
Deposition date deposition_date2021-01-25
Structure title titleCrystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A:Q38L mutant of cellular retinol binding protein II complex with all-trans-retinal
Keywords keywordshCRBPII, Q4A, Q38L, isomerization, retinal, all-trans-retinal, rhodopsin, bacteriorhodopsin, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.97
Radius of gyration Rg (electron density) rg_electron20.96
Forward intensity I(0) i017049100.00
Molecular weight molecular_weight31872.0 kDa
Excluded volume excluded_volume40157 ų
Envelope volume envelope_volume46748 ų
Hydration-shell volume shell_volume19421 ų
Envelope diameter envelope_diameter70.9
Shell Rg shell_rg26.33
Envelope Rg envelope_rg21.11
Shape Rg shape_rg20.98
Total Rg total_rg21.65
Total atoms total_atoms2268
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 dmax71.9
Rg (real space) rg_real22.03
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real1.7050e+07
I(0) uncertainty (real space) i0_real_error1.9470e+05
Rg (reciprocal space) rg_reciprocal22.02
I(0) (reciprocal space) i0_reciprocal17050000.0000
Solution quality estimate total_estimate0.8808
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4086000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7lhma_
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_idd7lhmb_
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

8. Citations (1)

9. Files and Curves (10)