6mlb

Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F mutant of human cellular retinol binding protein II

Method: X-RAY DIFFRACTION Dmax: 102.4 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–134 Chain C; UniProt 2–134 Fragment:Q108K, K40L, T51F GOL GLYCEROL × 1 ACT ACETATE ION × 2 RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;PEG 4000, ammonium acetate, sodium acetate Resolution 2.15 Å R-free 0.302
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–134 Chain D; UniProt 2–134 Fragment:Q108K, K40L, T51F GOL GLYCEROL × 3 ACT ACETATE ION × 3 RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;PEG 4000, ammonium acetate, sodium acetate Resolution 2.15 Å R-free 0.302

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 Author chain C; PDBConstruct 1–133; UniProt 2–134 Author chain D; 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 6mlb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6mlb
Deposition date deposition_date2018-09-27
Structure title titleCrystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F mutant of human cellular retinol binding protein II
Keywords keywordsiLBP, Protein Switch, 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_guinier30.22
Radius of gyration Rg (electron density) rg_electron29.76
Forward intensity I(0) i064892000.00
Molecular weight molecular_weight63047.0 kDa
Excluded volume excluded_volume78711 ų
Envelope volume envelope_volume99900 ų
Hydration-shell volume shell_volume30066 ų
Envelope diameter envelope_diameter103.4
Shell Rg shell_rg34.71
Envelope Rg envelope_rg29.64
Shape Rg shape_rg29.77
Total Rg total_rg30.17
Total atoms total_atoms4442
Residues n_residues532
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 dmax102.4
Rg (real space) rg_real30.37
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real6.4890e+07
I(0) uncertainty (real space) i0_real_error9.4610e+05
Rg (reciprocal space) rg_reciprocal30.30
I(0) (reciprocal space) i0_reciprocal64890000.0000
Solution quality estimate total_estimate0.8629
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.459
Kurtosis Kurtosis kurtosis-0.302
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27310000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.902

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6mlba_
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_idd6mlbb_
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_idd6mlbc_
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_idd6mlbd_
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 (4 domains)

Domain ID domain_id6mlbA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mlbB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mlbC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mlbD00
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)