4iap

Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae

Method: X-RAY DIFFRACTION Dmax: 80.4 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3

Saccharomyces cerevisiae

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–161 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–161 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–161 Chain B; UniProt 2–161 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274

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.

721 other PDB entries and 844 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 20–179; UniProt 2–161 Author chain B; PDBConstruct 20–179; UniProt 2–161

Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3

Saccharomyces cerevisiae

UniProt P38713

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 221–233 Chain A; UniProt 237–315 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 221–233 Chain B; UniProt 237–315 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 221–233 Chain A; UniProt 237–315 Chain B; UniProt 221–233 Chain B; UniProt 237–315 Fragment:PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation:D1020N, C1054T, C1097A SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.30 Å R-free 0.274

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OSH3_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–17; UniProt 221–233 Author chain A; PDBConstruct 182–260; UniProt 237–315 Author chain B; PDBConstruct 5–17; UniProt 221–233 Author chain B; PDBConstruct 182–260; UniProt 237–315

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 4iap

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4iap
Deposition date deposition_date2012-12-07
Structure title titleCrystal structure of PH domain of Osh3 from Saccharomyces cerevisiae
Keywords keywordsPH domain, beta sandwitch, targeting, phosphoinositides, LIPID BINDING PROTEIN- HYDRORASE complex; LIPID BINDING PROTEIN/ HYDRORASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.81
Radius of gyration Rg (electron density) rg_electron25.74
Forward intensity I(0) i060270600.00
Molecular weight molecular_weight59508.0 kDa
Excluded volume excluded_volume74271 ų
Envelope volume envelope_volume92611 ų
Hydration-shell volume shell_volume29821 ų
Envelope diameter envelope_diameter82.4
Shell Rg shell_rg33.17
Envelope Rg envelope_rg25.34
Shape Rg shape_rg25.72
Total Rg total_rg26.62
Total atoms total_atoms4180
Residues n_residues512
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 dmax80.4
Rg (real space) rg_real26.67
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real6.0270e+07
I(0) uncertainty (real space) i0_real_error7.8930e+05
Rg (reciprocal space) rg_reciprocal26.71
I(0) (reciprocal space) i0_reciprocal60270000.0000
Solution quality estimate total_estimate0.9076
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9314000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4iapA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4iapA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id4iapB01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4iapB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)