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- PDB-3g3t: Crystal structure of a eukaryotic polyphosphate polymerase in com... -

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Basic information

Entry
Database: PDB / ID: 3g3t
TitleCrystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate
ComponentsVacuolar transporter chaperone 4
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 / 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
PHOSPHATE ION / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLenherr, E.D. / Hothorn, 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
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,2166
Polymers34,7741
Non-polymers4425
Water4,378243
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.110, 136.110, 84.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 34773.754 Da / Num. of mol.: 1 / Fragment: UNP residues 189-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: J1345, PHM3, VTC4, YJL012C / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P47075
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1 M Na+/K+ phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2008
RadiationMonochromator: high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.85→48.3 Å / Num. all: 39665 / Num. obs: 39665 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 20.9 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.089 / Net I/σ(I): 28.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 5 / Num. unique all: 5697 / Rsym value: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3g3q

3g3q


Resolution: 1.85→39.647 Å / SU ML: 0.25 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1983 5 %RANDOM
Rwork0.1945 ---
obs0.1964 39660 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.52 Å2 / ksol: 0.389 e/Å3
Refinement stepCycle: LAST / Resolution: 1.85→39.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 24 243 2603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.1
X-RAY DIFFRACTIONf_bond_d0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.27161400.21582643X-RAY DIFFRACTION100
1.8963-1.94750.22121390.18932644X-RAY DIFFRACTION100
1.9475-2.00480.25431390.18212657X-RAY DIFFRACTION100
2.0048-2.06960.24021390.18252624X-RAY DIFFRACTION100
2.0696-2.14350.23261400.19062663X-RAY DIFFRACTION100
2.1435-2.22930.26251400.18212663X-RAY DIFFRACTION100
2.2293-2.33080.23291390.18112642X-RAY DIFFRACTION100
2.3308-2.45360.21911410.18452678X-RAY DIFFRACTION100
2.4536-2.60730.2171410.18282680X-RAY DIFFRACTION100
2.6073-2.80860.25671410.20422687X-RAY DIFFRACTION100
2.8086-3.09120.28011420.21072697X-RAY DIFFRACTION100
3.0912-3.53820.20911430.19022715X-RAY DIFFRACTION100
3.5382-4.45680.19161460.16712767X-RAY DIFFRACTION100
4.4568-39.65620.24591530.21842917X-RAY DIFFRACTION100

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