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- PDB-3g3q: Crystal structure of a eukaryotic polyphosphate polymerase in com... -

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Basic information

Entry
Database: PDB / ID: 3g3q
TitleCrystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer
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: 2.64 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: Derived calculations / 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_conn / 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_conn.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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)72,59034
Polymers69,5482
Non-polymers3,04232
Water1,02757
1
A: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,19916
Polymers34,7741
Non-polymers1,42615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,39018
Polymers34,7741
Non-polymers1,61717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-146 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 87.260, 128.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 193:478 )
211chain B and (resseq 193:478 )

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE ARE 29 ORDERED PO4 UNITS IN THE STRUCTURE. THIS POLYPHOSPHATE CHAIN IS SEVERAL HUNDRED UNITS ...THERE ARE 29 ORDERED PO4 UNITS IN THE STRUCTURE. THIS POLYPHOSPHATE CHAIN IS SEVERAL HUNDRED UNITS LONG AND IS GENERATED DURING CRYSTALLIZATION FROM ATP

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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: 4.06 Å3/Da / Density % sol: 69.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 3350, 0.15 M (NH4)2SO4, 0.1 M Bis-Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2007
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.64→20 Å / Num. all: 32041 / Num. obs: 32041 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 78.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 18.5
Reflection shellResolution: 2.64→2.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5063 / Rsym value: 0.708 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3g3o

3g3o


Resolution: 2.64→19.824 Å / SU ML: 0.43 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1615 5.04 %RANDOM
Rwork0.2273 ---
obs0.2284 32012 99.86 %-
all-32041 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.033 Å2 / ksol: 0.315 e/Å3
Refinement stepCycle: LAST / Resolution: 2.64→19.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 132 57 4939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d0.7
X-RAY DIFFRACTIONf_bond_d0.004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2375X-RAY DIFFRACTIONPOSITIONAL
12B2375X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.71750.35221440.35482514X-RAY DIFFRACTION100
2.7175-2.8050.27811360.30882538X-RAY DIFFRACTION100
2.805-2.9050.35361360.28322551X-RAY DIFFRACTION100
2.905-3.02090.29451400.28852498X-RAY DIFFRACTION100
3.0209-3.15790.32671460.26922518X-RAY DIFFRACTION100
3.1579-3.32360.3021360.26662524X-RAY DIFFRACTION100
3.3236-3.53080.28071410.23962574X-RAY DIFFRACTION100
3.5308-3.80160.28671260.2312545X-RAY DIFFRACTION100
3.8016-4.1810.20931310.20142540X-RAY DIFFRACTION100
4.181-4.77860.21321260.17732530X-RAY DIFFRACTION100
4.7786-5.99280.2061320.19562540X-RAY DIFFRACTION100
5.9928-19.82490.18941210.19952525X-RAY DIFFRACTION99

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