SAXSdb — 4ic4

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

Oxysterol-binding protein homolog 3

Saccharomyces cerevisiae

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 605–996	Fragment：ORD (OSBP related domain), UNP residues 605-996	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1M MES-NaOH pH 6.0, 25% PEG1500, 0.1M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.234

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.

Other PDB	Difference from Current Entry 4IC4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IAP Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae Deposited 2012-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 221–233（13 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Chain A 237–315（79 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315)	Mutation：D1020N, C1054T, C1097A 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
4IAP Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae Deposited 2012-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 221–233（13 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Chain B 237–315（79 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315)	Mutation：D1020N, C1054T, C1097A 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
4IAP Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae Deposited 2012-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 221–233（13 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Chain A 237–315（79 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Chain B 221–233（13 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Chain B 237–315（79 aa） Fragment：PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315)	Mutation：D1020N, C1054T, C1097A Mutation：D1020N, C1054T, C1097A Mutation：D1020N, C1054T, C1097A 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
4INQ Crystal structure of Osh3 ORD in complex with PI(4)P from Saccharomyces cerevisiae Deposited 2013-01-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 605–996（392 aa） Fragment：ORD (OSBP related domain), UNP residues 605-996	Not recorded	PIF (2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1M MES-NaOH, 25% polyethyleneglycol(PEG) 1500, 0.1M MgCl2, 0.5mM PI(4)P, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.280

2 other PDB entries and 4 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 6–397； UniProt 605–996

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ic4
Deposition date deposition_date	2012-12-09
Structure title title	Crystal structure of Osh3 ORD from Saccharomyces cerevisiae
Keywords keywords	beta barrel, lipid transport, PI(4)P binding, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.75 Å
Radius of gyration Rg (electron density) rg_electron	20.54 Å
Forward intensity I(0) i0	29868900.00
Molecular weight molecular_weight	42992.0 kDa
Excluded volume excluded_volume	54251 Å³
Envelope volume envelope_volume	62958 Å³
Hydration-shell volume shell_volume	24884 Å³
Envelope diameter envelope_diameter	70.3 Å
Shell Rg shell_rg	27.97 Å
Envelope Rg envelope_rg	20.86 Å
Shape Rg shape_rg	20.49 Å
Total Rg total_rg	21.62 Å
Total atoms total_atoms	3041
Residues n_residues	372
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.5 Å
Rg (real space) rg_real	21.60 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.9870e+07
I(0) uncertainty (real space) i0_real_error	3.5720e+05
Rg (reciprocal space) rg_reciprocal	21.63 Å
I(0) (reciprocal space) i0_reciprocal	29870000.0000
Solution quality estimate total_estimate	0.8916
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.0 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.386
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8327000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	40.866 Å
Unit-cell length b length_b	89.200 Å
Unit-cell length c length_c	96.102 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	32.690 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2340

Description description	Oxysterol-binding protein homolog 3
Molecular weight formula_weight	45683.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3332

Crystal structure of Osh3 ORD from Saccharomyces cerevisiae

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

Oxysterol-binding protein homolog 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	291

fit	/app/data/saxs_computation/ic/4ic4/4ic4.fit
pddf	/app/data/pr_computation/ic/4ic4/4ic4.pr.out
profile	/app/data/saxs_computation/ic/4ic4/4ic4.dat