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- PDB-5h28: Crystal structure of Osh1 ANK domain from Saccharomyces cerevisia -

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Basic information

Entry
Database: PDB / ID: 5h28
TitleCrystal structure of Osh1 ANK domain from Saccharomyces cerevisia
ComponentsOxysterol-binding protein homolog 1
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer / ANK Nvj1
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / nucleus-vacuole junction / sterol transfer activity / Golgi trans cisterna / : / sterol transport / sterol binding / maintenance of cell polarity / piecemeal microautophagy of the nucleus / nuclear outer membrane ...Synthesis of bile acids and bile salts / nucleus-vacuole junction / sterol transfer activity / Golgi trans cisterna / : / sterol transport / sterol binding / maintenance of cell polarity / piecemeal microautophagy of the nucleus / nuclear outer membrane / vacuolar membrane / exocytosis / endocytosis / nuclear envelope / early endosome / Golgi membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / 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. / Ankyrin repeats (many copies) / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Ankyrin repeats (many copies) / 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
Oxysterol-binding protein homolog 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsIm, Y.J. / Manik, M.K. / Yang, H.S. / Tong, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2014R1A1A1003060 and 2015M2B2A4031729 Korea, Republic Of
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 17, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Oxysterol-binding protein homolog 1


Theoretical massNumber of molelcules
Total (without water)30,0461
Polymers30,0461
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14150 Å2
Unit cell
Length a, b, c (Å)29.465, 72.202, 49.008
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxysterol-binding protein homolog 1


Mass: 30046.475 Da / Num. of mol.: 1 / Fragment: UNP residues 12-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SWH1, OSH1, YAR042W, YAR044W / Plasmid: modified pHIS-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35845
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 1.73 Å3/Da / Density % sol: 28.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES-NaOH pH 7.0, 20% PEG 1500

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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 270 / Detector: CCD / Date: Jul 5, 2014 / Details: focusing mirror
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 80061 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.8 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 693450.38 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1588 5 %RANDOM
Rwork0.184 ---
obs0.184 32045 97.6 %-
Solvent computationBsol: 52.4845 Å2 / ksol: 0.37765 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å21.11 Å2
2---2.76 Å20 Å2
3---2.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: 1 / Resolution: 1.5→24.55 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 247 4.8 %
Rwork0.202 4912 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top

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