4zcb

Human CRBPII mutant - Y60W dimer

Method: X-RAY DIFFRACTION Dmax: 70.1 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 B; UniProt 2–134 Fragment:UNP residues 2-134 Mutation:Y60W No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;294 K;30% PEG 4000, 0.1M CH3COONa.3H2O, pH 4.6, 0.1M CH3COONH4 Resolution 1.70 Å R-free 0.239

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 200 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 4zcb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4zcb
Deposition date deposition_date2015-04-15
Structure title titleHuman CRBPII mutant - Y60W dimer
Keywords keywordsRETINOL-BINDING PROTEIN, DOMAIN SWAPPING DIMERIZATION, 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_guinier22.43
Radius of gyration Rg (electron density) rg_electron21.77
Forward intensity I(0) i017063100.00
Molecular weight molecular_weight30482.0 kDa
Excluded volume excluded_volume37774 ų
Envelope volume envelope_volume46196 ų
Hydration-shell volume shell_volume18628 ų
Envelope diameter envelope_diameter69.6
Shell Rg shell_rg26.88
Envelope Rg envelope_rg21.56
Shape Rg shape_rg21.78
Total Rg total_rg22.42
Total atoms total_atoms2148
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 dmax70.1
Rg (real space) rg_real22.47
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.7060e+07
I(0) uncertainty (real space) i0_real_error2.5490e+05
Rg (reciprocal space) rg_reciprocal22.47
I(0) (reciprocal space) i0_reciprocal17060000.0000
Solution quality estimate total_estimate0.8958
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.3
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3662000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.957

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4zcba_
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_idd4zcbb_
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_id4zcbA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id4zcbB00
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)