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- PDB-2zii: Crystal Structure of Yeast Vps74-N-term Truncation Variant -

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Basic information

Entry
Database: PDB / ID: 2zii
TitleCrystal Structure of Yeast Vps74-N-term Truncation Variant
ComponentsVacuolar protein sorting-associated protein 74
KeywordsPROTEIN TRANSPORT / beta hairpin / vps / golgi localization / vps74 / tetramer / Golgi apparatus / Phosphoprotein / Transport
Function / homology
Function and homology information


regulation of phosphatidylinositol dephosphorylation / Golgi vesicle budding / protein O-linked mannosylation / Golgi cisterna / protein retention in Golgi apparatus / Golgi to plasma membrane protein transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / phosphatidylinositol-4-phosphate binding / Golgi medial cisterna ...regulation of phosphatidylinositol dephosphorylation / Golgi vesicle budding / protein O-linked mannosylation / Golgi cisterna / protein retention in Golgi apparatus / Golgi to plasma membrane protein transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / phosphatidylinositol-4-phosphate binding / Golgi medial cisterna / Golgi cisterna membrane / Golgi organization / endoplasmic reticulum unfolded protein response / trans-Golgi network / Golgi membrane / Golgi apparatus / enzyme binding / nucleus / cytosol / cytoplasm
Similarity search - Function
yeast vps74-n-term truncation variant fold / yeast vps74-n-term truncation variant domain like / Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 74
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsSchmitz, K.R. / Li, S. / Setty, T.G. / Ferguson, K.M.
CitationJournal: Dev.Cell / Year: 2008
Title: Golgi localization of glycosyltransferases requires a Vps74p oligomer.
Authors: Schmitz, K.R. / Liu, J. / Li, S. / Setty, T.G. / Wood, C.S. / Burd, C.G. / Ferguson, K.M.
History
DepositionFeb 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 74
B: Vacuolar protein sorting-associated protein 74
C: Vacuolar protein sorting-associated protein 74
D: Vacuolar protein sorting-associated protein 74


Theoretical massNumber of molelcules
Total (without water)132,2044
Polymers132,2044
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-44 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.081, 104.081, 292.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Vacuolar protein sorting-associated protein 74


Mass: 33050.961 Da / Num. of mol.: 4 / Mutation: deletion of amino acids 1-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS74
Plasmid details: vector modified to include TEV cleavage site
Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06385
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 3350, 5% glycerol, 10mM citrate, 0.75mM KCl, 50mM EGTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 35872 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.142 / Χ2: 1.262 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.166.20.52935240.874100
3.16-3.296.20.4235000.918100
3.29-3.436.20.3335560.996100
3.43-3.626.20.25535421.13100
3.62-3.846.20.18435411.301100
3.84-4.146.10.13935791.321100
4.14-4.566.20.09835701.38100
4.56-5.216.10.09236231.397100
5.21-6.5760.09736441.244100
6.57-505.40.07537932.13698.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.05 Å49.1 Å
Translation3.05 Å49.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZIH
Resolution: 3.05→49.1 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / SU B: 17.324 / SU ML: 0.312 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1790 5 %RANDOM
Rwork0.22 ---
obs0.223 35793 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 3.05→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8588 0 0 2 8590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228713
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.97811831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41224.263373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.659151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4731561
X-RAY DIFFRACTIONr_chiral_restr0.1120.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026470
X-RAY DIFFRACTIONr_nbd_refined0.2440.24416
X-RAY DIFFRACTIONr_nbtor_refined0.320.26105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.24
X-RAY DIFFRACTIONr_mcbond_it0.621.55682
X-RAY DIFFRACTIONr_mcangle_it1.13428925
X-RAY DIFFRACTIONr_scbond_it1.42633353
X-RAY DIFFRACTIONr_scangle_it2.3954.52906
LS refinement shellResolution: 3.053→3.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 133 -
Rwork0.297 2465 -
all-2598 -
obs--99.96 %

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