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- PDB-5wvr: Crystal structure of Osh1 ORD domain in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 5wvr
TitleCrystal structure of Osh1 ORD domain in complex with cholesterol
ComponentsKLLA0C04147p
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer / cholesterol
Function / homology
Function and homology information


sterol transfer activity / maintenance of cell polarity / piecemeal microautophagy of the nucleus / exocytosis / endocytosis / lipid binding / membrane
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
CHOLESTEROL / KLLA0C04147p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIm, Y.J. / Manik, M.K. / Yang, H.S. / Tong, J.S.
CitationJournal: Structure / Year: 2017
Title: Structure of Yeast OSBP-Related Protein Osh1 Reveals Key Determinants for Lipid Transport and Protein Targeting at the Nucleus-Vacuole Junction
Authors: Manik, M.K. / Yang, H. / Tong, J. / Im, Y.J.
History
DepositionDec 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0C04147p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3436
Polymers50,5721
Non-polymers7715
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-18 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.174, 46.602, 73.103
Angle α, β, γ (deg.)90.00, 96.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KLLA0C04147p


Mass: 50571.898 Da / Num. of mol.: 1 / Fragment: UNP residues 808-1240 / Mutation: 1109-1111 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C04147g / Plasmid: modified pHIS-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUK7
#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine-HCl pH 9.0, 20% PEG 3350, 0.2M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2016
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20511 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 5.24 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2D

5h2d


Resolution: 2.2→22.19 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.85
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1014 4.95 %Random selection
Rwork0.191 ---
obs0.193 20491 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 48 162 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093573
X-RAY DIFFRACTIONf_angle_d1.0384834
X-RAY DIFFRACTIONf_dihedral_angle_d19.0862134
X-RAY DIFFRACTIONf_chiral_restr0.067497
X-RAY DIFFRACTIONf_plane_restr0.006617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1983-2.31410.25241480.21472712X-RAY DIFFRACTION96
2.3141-2.45890.30641220.22442794X-RAY DIFFRACTION97
2.4589-2.64840.27781430.22472770X-RAY DIFFRACTION98
2.6484-2.91440.27481440.23142795X-RAY DIFFRACTION98
2.9144-3.33490.22991550.19832797X-RAY DIFFRACTION98
3.3349-4.1970.20991460.15642794X-RAY DIFFRACTION98
4.197-22.1890.1931560.17572815X-RAY DIFFRACTION95

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