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- PDB-3g3u: Crystal structure of a eukaryotic polyphosphate polymerase in com... -

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Basic information

Entry
Database: PDB / ID: 3g3u
TitleCrystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate
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
PYROPHOSPHATE 2- / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHothorn, M.
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

Downloads & links

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Assembly

Deposited unit
A: Vacuolar transporter chaperone 4
B: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,90614
Polymers69,5482
Non-polymers1,35812
Water6,846380
1
A: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5107
Polymers34,7741
Non-polymers7366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3967
Polymers34,7741
Non-polymers6226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.440, 100.730, 102.490
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 4 / Phosphate metabolism protein 3


Mass: 34773.754 Da / Num. of mol.: 2 / 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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15 % PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, 10 % Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→20 Å / Num. all: 43477 / Num. obs: 43477 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 6890 / Rsym value: 0.622 / % possible all: 97.3

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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 3g3r

3g3r


Resolution: 2.07→19.768 Å / SU ML: 0.35 / σ(F): 1.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 2094 5.09 %Same reflections as for 3g3r
Rwork0.1988 ---
obs0.201 41135 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.368 Å2 / ksol: 0.342 e/Å3
Refinement stepCycle: LAST / Resolution: 2.07→19.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 71 380 5183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1
X-RAY DIFFRACTIONf_bond_d0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.09650.3691100.30792079X-RAY DIFFRACTION79
2.0965-2.12120.30871440.2842528X-RAY DIFFRACTION98
2.1212-2.1470.28371260.25732652X-RAY DIFFRACTION99
2.147-2.17420.25731540.24732575X-RAY DIFFRACTION100
2.1742-2.20270.30811340.2342661X-RAY DIFFRACTION100
2.2027-2.23290.31021530.24422557X-RAY DIFFRACTION100
2.2329-2.26470.33921210.23692672X-RAY DIFFRACTION100
2.2647-2.29850.271390.22982623X-RAY DIFFRACTION100
2.2985-2.33430.33821540.22662617X-RAY DIFFRACTION100
2.3343-2.37260.27981380.21652613X-RAY DIFFRACTION100
2.3726-2.41340.2971310.21982631X-RAY DIFFRACTION100
2.4134-2.45720.27221620.21922633X-RAY DIFFRACTION100
2.4572-2.50440.24851180.20952629X-RAY DIFFRACTION100
2.5044-2.55540.27281310.20562607X-RAY DIFFRACTION100
2.5554-2.61080.2551660.20272647X-RAY DIFFRACTION100
2.6108-2.67140.28321290.2162610X-RAY DIFFRACTION100
2.6714-2.73810.28821290.21652655X-RAY DIFFRACTION100
2.7381-2.81190.26131480.21442608X-RAY DIFFRACTION100
2.8119-2.89440.27591410.21012618X-RAY DIFFRACTION100
2.8944-2.98750.24031670.21382595X-RAY DIFFRACTION100
2.9875-3.09390.24981470.19822634X-RAY DIFFRACTION100
3.0939-3.21730.28491220.20412644X-RAY DIFFRACTION100
3.2173-3.3630.23241340.19282621X-RAY DIFFRACTION100
3.363-3.53940.18631510.16662618X-RAY DIFFRACTION100
3.5394-3.75970.17431380.16422621X-RAY DIFFRACTION100
3.7597-4.04770.1881280.16562662X-RAY DIFFRACTION100
4.0477-4.45080.19791210.16362602X-RAY DIFFRACTION100
4.4508-5.08530.18841110.14642683X-RAY DIFFRACTION100
5.0853-6.37110.2251790.1982587X-RAY DIFFRACTION100
6.3711-19.76860.22221620.18272600X-RAY DIFFRACTION100

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