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- PDB-5h2c: Crystal structure of Saccharomyces cerevisiae Osh1 ANK - Nvj1 -

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Basic information

Entry
Database: PDB / ID: 5h2c
TitleCrystal structure of Saccharomyces cerevisiae Osh1 ANK - Nvj1
Components
  • Nucleus-vacuole junction protein 1
  • Oxysterol-binding protein homolog 1
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer
Function / homology
Function and homology information


nucleus-vacuole junction assembly / 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 ...nucleus-vacuole junction assembly / 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 / nuclear periphery / protein localization / lipid metabolic process / 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 / Nucleus-vacuole junction protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.508 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 1.1May 17, 2017Group: Derived calculations
Revision 1.2Mar 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
B: Nucleus-vacuole junction protein 1


Theoretical massNumber of molelcules
Total (without water)34,1792
Polymers34,1792
Non-polymers00
Water00
1
A: Oxysterol-binding protein homolog 1

B: Nucleus-vacuole junction protein 1


Theoretical massNumber of molelcules
Total (without water)34,1792
Polymers34,1792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.896, 67.748, 107.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxysterol-binding protein homolog 1


Mass: 30994.525 Da / Num. of mol.: 1 / Fragment: UNP residues 7-274
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: Protein/peptide Nucleus-vacuole junction protein 1


Mass: 3184.562 Da / Num. of mol.: 1 / Fragment: UNP residues 139-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NVJ1, VAB36, YHR195W / Plasmid: modified pHIS-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38881

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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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Citrate-NaOH pH 5.0, 15% PEG 20000, 0.2M KNO3

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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: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 5793 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 50.61 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 17
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 7.3 / % possible all: 100

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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 / Resolution: 3.508→30.726 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.15
RfactorNum. reflection% reflectionSelection details
Rfree0.27 265 4.6 %Random selection
Rwork0.1836 ---
obs0.1878 5760 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.508→30.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 0 2145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052183
X-RAY DIFFRACTIONf_angle_d0.8792952
X-RAY DIFFRACTIONf_dihedral_angle_d20.7761344
X-RAY DIFFRACTIONf_chiral_restr0.045339
X-RAY DIFFRACTIONf_plane_restr0.004384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5076-4.41710.30051170.19222665X-RAY DIFFRACTION98
4.4171-30.72690.24891480.17692830X-RAY DIFFRACTION100

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