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- PDB-1zi7: Structure of truncated yeast oxysterol binding protein Osh4 -

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Basic information

Entry
Database: PDB / ID: 1zi7
TitleStructure of truncated yeast oxysterol binding protein Osh4
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 / piecemeal microautophagy of the nucleus / maintenance of cell polarity / 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 / piecemeal microautophagy of the nucleus / maintenance of cell polarity / 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 - #1150 / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Oxysterol-binding protein homolog 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 27, 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KES1 protein
B: KES1 protein
C: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0519
Polymers139,4753
Non-polymers5766
Water2,540141
1
A: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6843
Polymers46,4921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6843
Polymers46,4921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6843
Polymers46,4921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: KES1 protein
hetero molecules

A: KES1 protein
B: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0519
Polymers139,4753
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,y+1/2,-z1
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-95 kcal/mol
Surface area55430 Å2
MethodPISA
5
A: KES1 protein
B: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3676
Polymers92,9832
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-62 kcal/mol
Surface area37490 Å2
MethodPISA
6
A: KES1 protein
hetero molecules

C: KES1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3676
Polymers92,9832
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2480 Å2
ΔGint-54 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.903, 100.853, 117.624
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46491.566 Da / Num. of mol.: 3 / Fragment: Residues 30 - 434 / Mutation: 236RGYFS -> VD
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, MES, pH 6.0, 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: 0.9792 / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 78298 / Num. obs: 75232 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.066 / Net I/σ(I): 22.9
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 3.16 / Num. unique all: 8145 / Rsym value: 0.355 / % possible all: 96.2

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Processing

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

1zhx


Resolution: 2.5→45.11 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1816335.14 / 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
Rfree0.246 3818 5.1 %RANDOM
Rwork0.21 ---
all0.213 78298 --
obs0.21 75232 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.908 Å2 / ksol: 0.370563 e/Å3
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å2-9.29 Å2
2--4.01 Å20 Å2
3----7.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9702 0 30 141 9873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
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: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 598 5 %
Rwork0.285 11275 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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