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- PDB-4b2z: Structure of Osh6 in complex with phosphatidylserine -

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Basic information

Entry
Database: PDB / ID: 4b2z
TitleStructure of Osh6 in complex with phosphatidylserine
ComponentsOxysterol-binding protein homolog 6
KeywordsTRANSPORT PROTEIN / LIPID TRANSPORT
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / sterol homeostasis / phospholipid transporter activity / sterol binding / cortical endoplasmic reticulum / phosphatidylinositol-5-phosphate binding ...Synthesis of bile acids and bile salts / Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / sterol homeostasis / phospholipid transporter activity / sterol binding / cortical endoplasmic reticulum / phosphatidylinositol-5-phosphate binding / sterol metabolic process / maintenance of cell polarity / piecemeal microautophagy of the nucleus / phosphatidic acid binding / phospholipid transport / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / phosphatidylserine binding / exocytosis / endocytosis / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature.
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Chem-P5S / Oxysterol-binding protein homolog 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMaeda, K. / Anand, K. / Chiapparino, A. / Kumar, A. / Poletto, M. / Kaksonen, M. / Gavin, A.C.
CitationJournal: Nature / Year: 2013
Title: Interactome Map Uncovers Phosphatidylserine Transport by Oxysterol-Binding Proteins
Authors: Maeda, K. / Anand, K. / Chiapparino, A. / Kumar, A. / Poletto, M. / Kaksonen, M. / Gavin, A.C.
History
DepositionJul 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Sep 18, 2013Group: Database references
Revision 1.4Dec 12, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_ref
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 6
B: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4158
Polymers103,3302
Non-polymers2,0856
Water6,539363
1
A: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7074
Polymers51,6651
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7074
Polymers51,6651
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.000, 72.600, 122.900
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 36:191 OR RESSEQ 193:218 OR RESSEQ...
211CHAIN B AND (RESSEQ 35:191 OR RESSEQ 193:218 OR RESSEQ...

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxysterol-binding protein homolog 6


Mass: 51664.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OSH6, YKR003W, YK102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q02201

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Non-polymers , 5 types, 369 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine / Phosphatidylserine


Mass: 792.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO10P
#4: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES PH6.5, 13% PEG6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 65896 / % possible obs: 91.8 % / Observed criterion σ(I): 1.63 / Redundancy: 3.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.6 / % possible all: 59

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZHT

1zht


Resolution: 1.95→46.566 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1318 2 %
Rwork0.1975 --
obs0.1982 65887 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.39 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--4.186 Å20 Å2-4.3005 Å2
2---2.9646 Å20 Å2
3---7.1506 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 133 363 7029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086832
X-RAY DIFFRACTIONf_angle_d1.2199216
X-RAY DIFFRACTIONf_dihedral_angle_d19.9822662
X-RAY DIFFRACTIONf_chiral_restr0.095963
X-RAY DIFFRACTIONf_plane_restr0.0061183
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2839X-RAY DIFFRACTIONPOSITIONAL
12B2839X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.02810.3029950.25344652X-RAY DIFFRACTION60
2.0281-2.12040.31371170.22015743X-RAY DIFFRACTION74
2.1204-2.23220.2631470.20857220X-RAY DIFFRACTION93
2.2322-2.3720.24411580.20117741X-RAY DIFFRACTION100
2.372-2.55520.25281590.20317781X-RAY DIFFRACTION100
2.5552-2.81230.25881600.2017837X-RAY DIFFRACTION100
2.8123-3.21910.20441590.19047790X-RAY DIFFRACTION100
3.2191-4.05540.20211600.1747842X-RAY DIFFRACTION100
4.0554-46.57940.21761630.18217963X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.9179 Å / Origin y: -17.9992 Å / Origin z: 30.9626 Å
111213212223313233
T0.0798 Å2-0.0099 Å2-0.0147 Å2-0.1168 Å20.0052 Å2--0.0765 Å2
L0.5846 °20.0597 °2-0.0103 °2-0.3148 °2-0.099 °2--0.506 °2
S0.0117 Å °0.1578 Å °0.0427 Å °-0.0134 Å °0.0409 Å °0.014 Å °0.0467 Å °0.0334 Å °-0.0442 Å °
Refinement TLS groupSelection details: ALL

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