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- PDB-3g3o: Crystal structure of the cytoplasmic tunnel domain in yeast Vtc2p -

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Basic information

Entry
Database: PDB / ID: 3g3o
TitleCrystal structure of the cytoplasmic tunnel domain in yeast Vtc2p
ComponentsVacuolar transporter chaperone 2
KeywordsBIOSYNTHETIC PROTEIN / polyphosphate polymerase / polyphosphate kinase / VTC complex / vacuolar transporter chaperone / tunnel enzyme / Membrane / Phosphoprotein / Transmembrane / Vacuole
Function / homology
Function and homology information


: / vacuolar transporter chaperone complex / polyphosphate biosynthetic process / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding / fungal-type vacuole membrane / protein localization ...: / vacuolar transporter chaperone complex / polyphosphate biosynthetic process / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding / fungal-type vacuole membrane / protein localization / membrane => GO:0016020 / calmodulin binding / endoplasmic reticulum
Similarity search - Function
VTC, catalytic tunnel domain / Domain of unknown function DUF202 / VTC domain / Domain of unknown function (DUF202) / VTC domain / mRNA Triphosphatase Cet1; Chain A / SPX domain / SPX domain profile. / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Vacuolar transporter chaperone 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHothorn, M. / Scheffzek, K.
CitationJournal: Science / Year: 2009
Title: Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase.
Authors: Hothorn, M. / Neumann, H. / Lenherr, E.D. / Wehner, M. / Rybin, V. / Hassa, P.O. / Uttenweiler, A. / Reinhardt, M. / Schmidt, A. / Seiler, J. / Ladurner, A.G. / Herrmann, C. / Scheffzek, K. / Mayer, A.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar transporter chaperone 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7234
Polymers45,4351
Non-polymers2883
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.200, 74.590, 80.470
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 Vacuolar transporter chaperone 2 / Phosphate metabolism protein 1


Mass: 45435.031 Da / Num. of mol.: 1 / Fragment: UNP residues 183-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PHM1, VTC2, YFL004W / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P43585
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22 % PEG 4000, 0.2 M Li2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9780, 0.97790 0.9742
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2005
RadiationMonochromator: double Silicon (111) crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97791
30.97421
ReflectionResolution: 2.1→43.4 Å / Num. obs: 25562 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.117 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 7526 / Rsym value: 0.62 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→37.295 Å / SU ML: 0.31 / σ(F): 1.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1301 5.09 %RANDOM
Rwork0.1985 ---
obs0.2004 25559 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.717 Å2 / ksol: 0.374 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→37.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 15 206 2598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.48
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18180.28171410.22032500X-RAY DIFFRACTION94
2.1818-2.28110.22111460.18592661X-RAY DIFFRACTION100
2.2811-2.40140.23821470.18062673X-RAY DIFFRACTION100
2.4014-2.55180.24211410.18622692X-RAY DIFFRACTION100
2.5518-2.74880.24941440.19422677X-RAY DIFFRACTION100
2.7488-3.02530.21611470.19922695X-RAY DIFFRACTION100
3.0253-3.46270.23011530.19292715X-RAY DIFFRACTION100
3.4627-4.36160.17751590.17382745X-RAY DIFFRACTION100
4.3616-37.30090.26771230.20922900X-RAY DIFFRACTION100

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