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- PDB-5h2d: Crystal structure of Osh1 ORD domain in complex with ergosterol -

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Basic information

Entry
Database: PDB / ID: 5h2d
TitleCrystal structure of Osh1 ORD domain in complex with ergosterol
ComponentsKLLA0C04147p
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer / ergosterol
Function / homology
Function and homology information


sterol transfer activity / sterol binding / perinuclear endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / exocytosis / endocytosis / nuclear envelope / plasma membrane / cytosol
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
ERGOSTEROL / KLLA0C04147p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionOct 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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)51,3536
Polymers50,5721
Non-polymers7815
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.129, 47.207, 73.000
Angle α, β, γ (deg.)90.00, 96.24, 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 1808-1240 / 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-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44O
#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.: 461 / 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: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 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: 1.6→50 Å / Num. obs: 54668 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.3 / % possible all: 99.2

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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: 4INQ

4inq


Resolution: 1.6→37.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.98
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1999 3.66 %Random selection
Rwork0.177 ---
obs0.178 54644 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 49 461 3950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063581
X-RAY DIFFRACTIONf_angle_d0.9054847
X-RAY DIFFRACTIONf_dihedral_angle_d18.6542185
X-RAY DIFFRACTIONf_chiral_restr0.056498
X-RAY DIFFRACTIONf_plane_restr0.007620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5993-1.63930.24441380.20133642X-RAY DIFFRACTION96
1.6393-1.68360.26321420.19183713X-RAY DIFFRACTION99
1.6836-1.73320.21731410.18863740X-RAY DIFFRACTION99
1.7332-1.78910.22891430.18583745X-RAY DIFFRACTION99
1.7891-1.85310.23761400.18853706X-RAY DIFFRACTION99
1.8531-1.92730.23351430.18413768X-RAY DIFFRACTION99
1.9273-2.0150.22741430.18683741X-RAY DIFFRACTION100
2.015-2.12120.23441420.18213741X-RAY DIFFRACTION99
2.1212-2.25410.23121440.17443793X-RAY DIFFRACTION100
2.2541-2.42810.19191420.17983761X-RAY DIFFRACTION100
2.4281-2.67240.22321450.18393787X-RAY DIFFRACTION100
2.6724-3.05890.19191450.18653808X-RAY DIFFRACTION100
3.0589-3.85330.19621440.1633811X-RAY DIFFRACTION100
3.8533-37.28980.1881470.16533889X-RAY DIFFRACTION99

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