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- PDB-5iiq: Structure of the SPX-TTM domain fragment of the yeast inorganic p... -

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Basic information

Entry
Database: PDB / ID: 5iiq
TitleStructure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).
ComponentsVacuolar transporter chaperone 4
KeywordsTRANSFERASE / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / chaperone
Function / homology
Function and homology information


vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / polyphosphate metabolic process / vacuolar transport / fungal-type vacuole membrane / inositol hexakisphosphate binding ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / polyphosphate metabolic process / vacuolar transport / fungal-type vacuole membrane / inositol hexakisphosphate binding / vacuolar membrane / autophagosome membrane / cell periphery / cytoplasmic vesicle / cell cortex / calmodulin binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
VTC, catalytic tunnel domain / Domain of unknown function DUF202 / VTC domain / VTC domain superfamily / : / Domain of unknown function (DUF202) / VTC domain / mRNA Triphosphatase Cet1; Chain A / SPX domain / SPX domain profile. ...VTC, catalytic tunnel domain / Domain of unknown function DUF202 / VTC domain / VTC domain superfamily / : / 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
PYROPHOSPHATE 2- / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Reseacrh Council310856 Switzerland
CitationJournal: Science / Year: 2016
Title: Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.
Authors: Wild, R. / Gerasimaite, R. / Jung, J.Y. / Truffault, V. / Pavlovic, I. / Schmidt, A. / Saiardi, A. / Jessen, H.J. / Poirier, Y. / Hothorn, M. / Mayer, A.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 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

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Assembly

Deposited unit
A: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4165
Polymers56,9521
Non-polymers4644
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-44 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.041, 92.041, 301.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Vacuolar transporter chaperone 4 / Phosphate metabolism protein 3


Mass: 56951.621 Da / Num. of mol.: 1 / Fragment: SPX domain- TTM domain, UNP residues 2-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTC4, PHM3, YJL012C, J1345 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P47075
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2

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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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.5M AmSO4, 4% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 15492 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 20.7 % / Biso Wilson estimate: 99.42 Å2 / CC1/2: 1 / Rsym value: 0.108 / Net I/σ(I): 28.4
Reflection shellResolution: 3.03→3.21 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 2.99 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g3r

3g3r


Resolution: 3.03→19.88 Å / Cor.coef. Fo:Fc: 0.9234 / Cor.coef. Fo:Fc free: 0.9174 / SU R Cruickshank DPI: 3.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.395 / SU Rfree Cruickshank DPI: 0.395
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 774 5 %RANDOM
Rwork0.2246 ---
obs0.2266 15479 99.74 %-
Displacement parametersBiso mean: 94.81 Å2
Baniso -1Baniso -2Baniso -3
1--6.0116 Å20 Å20 Å2
2---6.0116 Å20 Å2
3---12.0232 Å2
Refine analyzeLuzzati coordinate error obs: 0.766 Å
Refinement stepCycle: 1 / Resolution: 3.03→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 24 0 3823
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083902HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15280HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1388SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3902HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion19.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4266SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.24 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 134 4.98 %
Rwork0.2665 2558 -
all0.2716 2692 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 38.0344 Å / Origin y: 35.3267 Å / Origin z: 302.91 Å
111213212223313233
T-0.4124 Å2-0.0235 Å20.0716 Å2-0.2787 Å2-0.0261 Å2--0.0351 Å2
L0.0418 °2-0.0379 °20.4371 °2-0.3585 °20.0397 °2--2.6246 °2
S-0.072 Å °-0.0221 Å °0.012 Å °-0.0107 Å °0.2223 Å °0.1549 Å °0.1636 Å °-0.2283 Å °-0.1504 Å °
Refinement TLS groupSelection details: { A|* }

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