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- PDB-3q8g: Resurrection of a functional phosphatidylinositol transfer protei... -

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Basic information

Entry
Database: PDB / ID: 3q8g
TitleResurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution
ComponentsCRAL-TRIO domain-containing protein YKL091C
KeywordsSIGNALING PROTEIN / CRAL-TRIO / string motif / directed evolution / PIPT / SEC14 / phospholipid transporter / lipid / phosphatidylinositol / phosphatidylcholine
Function / homology
Function and homology information


phosphatidylcholine binding / phosphatidylinositol binding / nucleus
Similarity search - Function
N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / CRAL-TRIO domain-containing protein YKL091C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOrtlund, E.A. / Schaaf, G. / Bankaitis, V.A.
CitationJournal: Mol.Biol.Cell / Year: 2011
Title: Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution.
Authors: Schaaf, G. / Dynowski, M. / Mousley, C.J. / Shah, S.D. / Yuan, P. / Winklbauer, E.M. / de Campos, M.K. / Trettin, K. / Quinones, M.C. / Smirnova, T.I. / Yanagisawa, L.L. / Ortlund, E.A. / Bankaitis, V.A.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Non-polymer description
Revision 2.0May 31, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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

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Assembly

Deposited unit
A: CRAL-TRIO domain-containing protein YKL091C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1923
Polymers37,3561
Non-polymers8362
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.503, 71.388, 99.650
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 CRAL-TRIO domain-containing protein YKL091C


Mass: 37355.727 Da / Num. of mol.: 1 / Mutation: E126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKL091C / Production host: Escherichia coli (E. coli) / References: UniProt: P33324
#2: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25.5 % (w/v) PEG 4000, 11.9 % (v/v) glycerol and 170 mM sodium acetate, 85 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 8, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 31603 / Num. obs: 29675 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.306 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2590 / % possible all: 78.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.069 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22895 1591 5 %RANDOM
Rwork0.19164 ---
all0.19353 31603 --
obs0.19353 -93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--0.35 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 50 222 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222653
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9913579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7995313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40823.629124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16115474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3471517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211988
X-RAY DIFFRACTIONr_mcbond_it0.7261.51542
X-RAY DIFFRACTIONr_mcangle_it1.38122512
X-RAY DIFFRACTIONr_scbond_it2.13731111
X-RAY DIFFRACTIONr_scangle_it3.3884.51063
X-RAY DIFFRACTIONr_rigid_bond_restr1.28632653
LS refinement shellResolution: 1.8→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 92 -
Rwork0.198 1772 -
obs-2590 75.93 %

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