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- PDB-1aua: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES C... -

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Basic information

Entry
Database: PDB / ID: 1aua
TitlePHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES CEREVISIAE
ComponentsPHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P
KeywordsPHOSPHOLIPID-BINDING PROTEIN / PERIPHERAL GOLGI MEMBRANE PROTEIN / PHOSPHOLIPID EXCHANGE / GOLGI-DERIVED SECRETORY VESICLE BIOGENESIS
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 / Golgi to vacuole transport / ascospore formation / post-Golgi vesicle-mediated transport / phosphatidylinositol metabolic process / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / Golgi to vacuole transport / ascospore formation / post-Golgi vesicle-mediated transport / phosphatidylinositol metabolic process / phospholipid transport / Golgi to plasma membrane protein transport / Golgi membrane / Golgi apparatus / cytoplasm / cytosol
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
SEC14 cytosolic factor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsSha, B. / Phillips, S.E. / Bankaitis, V.A. / Luo, M.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol-transfer protein.
Authors: Sha, B. / Phillips, S.E. / Bankaitis, V.A. / Luo, M.
History
DepositionAug 20, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6303
Polymers34,0461
Non-polymers5852
Water95553
1
A: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P
hetero molecules

A: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2616
Polymers68,0912
Non-polymers1,1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)88.971, 88.971, 111.339
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 PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P


Mass: 34045.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC14 / Plasmid: PQE-31 / Gene (production host): SEC14 / Production host: Escherichia coli (E. coli) / Strain (production host): KK2186 / References: UniProt: P24280
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.6 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.2
Details: 3% PEG 3350, 1% N-OCTYL B-D-GLUCOPYRANOSIDE, 10 MM HEPES, 150MM KCL, PH 7.2
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMHEPES1drop
3150 mM1dropKCl
410 mMHEPES1reservoir
5150 mM1reservoirKCl
62 %n-octyl beta-D-glucopyranoside1reservoir
73 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 16736 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.051 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 8 / Rsym value: 0.265 / % possible all: 80
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE PARAMETER AND TOPOLOGY FILES ARE AVAILABLE FROM DR. B.SHA.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1083 7 %RANDOM
Rwork0.211 ---
obs0.211 16259 90.8 %-
Displacement parametersBiso mean: 47.24 Å2
Refine analyzeLuzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 40 53 2586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.422
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.218
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.295 64 3.5 %
Rwork0.354 2029 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.218
LS refinement shell
*PLUS
Rfactor obs: 0.354

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