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- PDB-4iap: Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4iap
TitleCrystal structure of PH domain of Osh3 from Saccharomyces cerevisiae
ComponentsOxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
KeywordsLIPID BINDING PROTEIN/ HYDRORASE / PH domain / beta sandwitch / targeting / phosphoinositides / LIPID BINDING PROTEIN- HYDRORASE complex
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / sterol transfer activity / pseudohyphal growth / karyogamy involved in conjugation with cellular fusion / sterol transport / invasive growth in response to glucose limitation / : / sterol binding / ER to Golgi ceramide transport / perinuclear endoplasmic reticulum ...Synthesis of bile acids and bile salts / sterol transfer activity / pseudohyphal growth / karyogamy involved in conjugation with cellular fusion / sterol transport / invasive growth in response to glucose limitation / : / sterol binding / ER to Golgi ceramide transport / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / cholesterol binding / exocytosis / viral release from host cell by cytolysis / peptidoglycan catabolic process / endocytosis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / lipid binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pleckstrin homology domain 8 / Pleckstrin homology domain / GOLD domain superfamily / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Lysozyme - #40 ...Pleckstrin homology domain 8 / Pleckstrin homology domain / GOLD domain superfamily / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Lysozyme - #40 / PH-domain like / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Lysozyme / Lysozyme-like domain superfamily / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endolysin / Oxysterol-binding protein homolog 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTong, J. / Im, Y.J.
CitationJournal: Structure / Year: 2013
Title: Structure of osh3 reveals a conserved mode of phosphoinositide binding in oxysterol-binding proteins
Authors: Tong, J. / Yang, H. / Yang, H. / Eom, S.H. / Im, Y.J.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Source and taxonomy
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Nov 8, 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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: Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
B: Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26110
Polymers59,4922
Non-polymers7698
Water1,856103
1
A: Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2266
Polymers29,7461
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0344
Polymers29,7461
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-11 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.033, 91.307, 84.130
Angle α, β, γ (deg.)90.00, 81.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3 / Lysis protein / Lysozyme / Muramidase


Mass: 29746.031 Da / Num. of mol.: 2
Fragment: PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315)
Mutation: D1020N, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: ATCC 204508 / S288c / Gene: OSH3, YHR073W / Plasmid: modifed pHIS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38713, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE SEQUENCE CONFLICTS IN THE UNP SEQUENCE REFERENCE P00720.

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 33493 / Num. obs: 32983 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1666 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T4 Lysozyme 212L

212l


Resolution: 2.3→40.02 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1788889.68 / 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
Rfree0.274 1629 5 %RANDOM
Rwork0.242 ---
obs0.242 32446 99.4 %-
all-34075 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8257 Å2 / ksol: 0.328213 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.33 Å20 Å23.93 Å2
2--2.48 Å20 Å2
3---0.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 40 103 4283
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
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: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 261 4.9 %
Rwork0.288 5061 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top

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