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- PDB-1zhw: Structure of yeast oxysterol binding protein Osh4 in complex with... -

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Basic information

Entry
Database: PDB / ID: 1zhw
TitleStructure of yeast oxysterol binding protein Osh4 in complex with 20-hydroxycholesterol
ComponentsKES1 protein
KeywordsLIPID BINDING PROTEIN / oxysterol / sterol binding protein
Function / homology
Function and homology information


Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / ER to Golgi ceramide transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / piecemeal microautophagy of the nucleus / sphingolipid metabolic process / phosphatidic acid binding ...Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / ER to Golgi ceramide transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / piecemeal microautophagy of the nucleus / sphingolipid metabolic process / phosphatidic acid binding / oxysterol binding / phosphatidylinositol-4-phosphate binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / endocytosis / Golgi membrane / intracellular membrane-bounded organelle / lipid binding / membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #2720 / Porin - #120 / Alpha-Beta Plaits - #3490 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Porin ...Helix Hairpins - #2720 / Porin - #120 / Alpha-Beta Plaits - #3490 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Porin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Helix Hairpins / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
20-HYDROXYCHOLESTEROL / LEAD (II) ION / Oxysterol-binding protein homolog 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIm, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H.
CitationJournal: Nature / Year: 2005
Title: Structural mechanism for sterol sensing and transport by OSBP-related proteins
Authors: Im, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H.
History
DepositionApr 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5083
Polymers49,8981
Non-polymers6102
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.300, 94.910, 65.400
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KES1 protein / Oxysterol-binding protein homolog 4


Mass: 49898.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OSH4 / Plasmid: modified pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35844
#2: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-HC2 / 20-HYDROXYCHOLESTEROL / (3BETA,20R)-CHOLEST-5-ENE-3,20-DIOL


Mass: 402.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9686 / Wavelength: 0.9686 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 55662 / Num. obs: 53180 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.041 / Net I/σ(I): 26.4
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.37 / Num. unique all: 4592 / Rsym value: 0.32 / % possible all: 84.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1ZHX

1zhx


Resolution: 1.7→38.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 848892.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2535 5 %RANDOM
Rwork0.214 ---
all0.221 53180 --
obs0.214 50696 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6798 Å2 / ksol: 0.390044 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å22.79 Å2
2--4.26 Å20 Å2
3----4.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 30 262 3806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
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: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 344 5.1 %
Rwork0.28 6422 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION320hc.par20hc.par
X-RAY DIFFRACTION4ion.paramion.top

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