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- PDB-2zih: Crystal Structure of Yeast Vps74 -

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Basic information

Entry
Database: PDB / ID: 2zih
TitleCrystal Structure of Yeast Vps74
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 / enzyme binding / Golgi apparatus / nucleus / cytoplasm / cytosol
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 / MAD / Resolution: 2.8 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 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)157,9164
Polymers157,9164
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-46 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.688, 102.688, 292.323
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: 39478.875 Da / Num. of mol.: 4
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.: 5 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG 3350, 5% ethylene glycol, 50mM MES, 50mM NaCl, 50mM CaCl2, 10mM EGTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97926, 0.97942, 0.94927
SYNCHROTRONAPS 23-ID-D21.036
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 9, 2007
MARMOSAIC 300 mm CCD2CCDApr 9, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979421
30.949271
41.0361
ReflectionRedundancy: 10.2 % / Av σ(I) over netI: 6.9 / Number: 254363 / Rmerge(I) obs: 0.14 / Χ2: 1.76 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 24850 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.310.0653.95610
5.817.3299.610.1252.32210.7
5.085.8199.710.141.79610.9
4.615.0899.610.1281.69811
4.284.6199.510.1341.57411.1
4.034.2899.510.1641.33311.1
3.834.0399.410.2181.20311
3.663.8399.210.2821.09810.5
3.523.6698.610.3781.0979.2
3.43.5295.410.4561.0316.6
ReflectionResolution: 2.8→50 Å / Num. obs: 43558 / % possible obs: 97.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.093 / Χ2: 2.024 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.92.80.34236581.28283.8
2.9-3.023.50.30742271.28295.2
3.02-3.154.70.28143431.25499.3
3.15-3.325.60.22544081.29299.9
3.32-3.535.90.1744191.61299.8
3.53-3.85.90.12344102.00599.7
3.8-4.1860.08344452.16699.8
4.18-4.7960.06744682.39899.7
4.79-6.035.90.07145372.73499.6
6.03-505.60.0546433.05697.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→37.99 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.113 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.732 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.302 2198 5.1 %RANDOM
Rwork0.233 ---
obs0.237 43510 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.287 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20.97 Å20 Å2
2--1.94 Å20 Å2
3----2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8536 0 0 5 8541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228665
X-RAY DIFFRACTIONr_angle_refined_deg1.641.97611772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31751121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03923.906361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.366151451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0331564
X-RAY DIFFRACTIONr_chiral_restr0.1260.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026429
X-RAY DIFFRACTIONr_nbd_refined0.2440.24133
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.23
X-RAY DIFFRACTIONr_mcbond_it0.6171.55676
X-RAY DIFFRACTIONr_mcangle_it1.13728916
X-RAY DIFFRACTIONr_scbond_it1.57933296
X-RAY DIFFRACTIONr_scangle_it2.6464.52856
LS refinement shellResolution: 2.8→2.861 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 116 -
Rwork0.329 1820 -
all-1936 -
obs--69.32 %

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