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- PDB-6f0e: Structure of yeast Sec14p with a picolinamide compound -

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Basic information

Entry
Database: PDB / ID: 6f0e
TitleStructure of yeast Sec14p with a picolinamide compound
ComponentsSEC14 cytosolic factor
KeywordsLIPID BINDING PROTEIN / Sec14p / lipid transfer protein / chemogenomics / target identification / functional variomics / co-crystal / antifungal / benzamide / picolinamide
Function / homology
Function and homology information


negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport / Golgi membrane / Golgi apparatus / cytosol / cytoplasm
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. ...: / 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
Chem-C8K / SEC14 cytosolic factor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHong, Z. / Johnen, P. / Schaaf, G. / Bono, F.
Funding support United States, Germany, 6items
OrganizationGrant numberCountry
National Institutes of HealthGM44530 United States
Robert A. Welch FoundationBE-0017 United States
German Research FoundationSCHA 1274/2-1, SFB 1101/TP A05 and SCHA 1274/4-1 Germany
Max Planck Society(FP7/2007-2013 Germany
European Research Council310957 Germany
German Research FoundationBO3588/2-1 Germany
CitationJournal: Cell Chem Biol / Year: 2018
Title: Target Identification and Mechanism of Action of Picolinamide and Benzamide Chemotypes with Antifungal Properties.
Authors: Pries, V. / Nocker, C. / Khan, D. / Johnen, P. / Hong, Z. / Tripathi, A. / Keller, A.L. / Fitz, M. / Perruccio, F. / Filipuzzi, I. / Thavam, S. / Aust, T. / Riedl, R. / Ziegler, S. / Bono, F. ...Authors: Pries, V. / Nocker, C. / Khan, D. / Johnen, P. / Hong, Z. / Tripathi, A. / Keller, A.L. / Fitz, M. / Perruccio, F. / Filipuzzi, I. / Thavam, S. / Aust, T. / Riedl, R. / Ziegler, S. / Bono, F. / Schaaf, G. / Bankaitis, V.A. / Waldmann, H. / Hoepfner, D.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4012
Polymers36,0481
Non-polymers3531
Water1629
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.077, 88.077, 109.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SEC14 cytosolic factor / Phosphatidylinositol/phosphatidylcholine transfer protein / PI/PC TP


Mass: 36047.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC14, PIT1, YMR079W, YM9582.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P24280
#2: Chemical ChemComp-C8K / ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-bromanyl-3-fluoranyl-pyridine-2-carboxamide


Mass: 353.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10BrFN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 129.5 mM sodium acetate, 64.8 mM TRIS, 10 % (w/v) PEG 4000, 20 % (v/v) glycerol, pH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29163 / % possible obs: 99.9 % / Redundancy: 10.62 % / Rrim(I) all: 0.227 / Net I/σ(I): 12.22
Reflection shellResolution: 2.6→2.76 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUA

1aua


Resolution: 2.6→44.412 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.64
RfactorNum. reflection% reflection
Rfree0.2255 1446 4.96 %
Rwork0.1993 --
obs0.2006 29133 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 21 9 2405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172461
X-RAY DIFFRACTIONf_angle_d1.3693338
X-RAY DIFFRACTIONf_dihedral_angle_d16.295907
X-RAY DIFFRACTIONf_chiral_restr0.12347
X-RAY DIFFRACTIONf_plane_restr0.009437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5996-2.69250.34881440.31982731X-RAY DIFFRACTION99
2.6925-2.80030.30331440.29312794X-RAY DIFFRACTION100
2.8003-2.92780.28871470.28382779X-RAY DIFFRACTION100
2.9278-3.08210.27981440.28312708X-RAY DIFFRACTION100
3.0821-3.27510.32771440.26462809X-RAY DIFFRACTION100
3.2751-3.52790.25231450.21242790X-RAY DIFFRACTION100
3.5279-3.88270.2191440.19412753X-RAY DIFFRACTION100
3.8827-4.44410.19321460.16262767X-RAY DIFFRACTION100
4.4441-5.59740.21251430.15352789X-RAY DIFFRACTION100
5.5974-44.41870.14781450.15812767X-RAY DIFFRACTION100

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