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

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Basic information

Entry
Database: PDB / ID: 5iig
TitleStructure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form A).
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
Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research 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)57,3215
Polymers56,9371
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-66 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.390, 145.390, 71.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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


Mass: 56936.605 Da / Num. of mol.: 1 / Fragment: SPX domain, UNP residues 2-480 / Mutation: E426N
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.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.5M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 16084 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 119.79 Å2 / CC1/2: 1 / Rsym value: 0.082 / Net I/σ(I): 20.22
Reflection shellResolution: 2.99→3.17 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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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: 2.99→48.22 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.9285 / SU R Cruickshank DPI: 1.852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.006 / SU Rfree Blow DPI: 0.394 / SU Rfree Cruickshank DPI: 0.401
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 797 4.96 %RANDOM
Rwork0.2438 ---
obs0.2452 16083 99.77 %-
Displacement parametersBiso mean: 113.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.4103 Å20 Å20 Å2
2---3.4103 Å20 Å2
3---6.8207 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: 1 / Resolution: 2.99→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 20 0 3871
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0243954HARMONIC0.5
X-RAY DIFFRACTIONt_angle_deg0.795347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1410SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes558HARMONIC5
X-RAY DIFFRACTIONt_it3954HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.48
X-RAY DIFFRACTIONt_other_torsion17.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion497SEMIHARMONIC5
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_contact4095SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2974 115 4.11 %
Rwork0.2787 2686 -
all0.2795 2801 -
obs--99.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04570.6298-1.70381.4408-0.46212.09360.03650.0558-0.0472-0.20090.0497-0.10110.16520.099-0.0862-0.22480.14340.01190.2681-0.1439-0.082895.4667129.98912.7762
20.5967-1.0581.59882.35160.77642.2670.00070.0004-0.01930.0088-0.0052-0.01040.02040.01870.0045-0.03320.00290.00790.126-0.01980.0153104.694138.0220.6714
35.98270.57590.69930.5484-0.25980.3102-0.016-0.1118-0.0184-0.04190.0827-0.10050.08430.0714-0.0666-0.0923-0.1224-0.07550.00040.0107-0.025857.0686120.9230.4379
44.42940.45711.03761.3453-0.71534.5495-0.09480.2272-0.0997-0.11880.19650.0978-0.13220.046-0.1017-0.1132-0.155-0.0045-0.221-0.0088-0.116248.6307122.85521.5555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|137 }
2X-RAY DIFFRACTION2{ A|138 - A|160 }
3X-RAY DIFFRACTION3{ A|161 - A|254 }
4X-RAY DIFFRACTION4{ A|255 - A|479 }

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