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- PDB-3g3r: Crystal structure of a eukaryotic polyphosphate polymerase in com... -

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Basic information

Entry
Database: PDB / ID: 3g3r
TitleCrystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+
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 / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding / fungal-type vacuole membrane / vacuolar membrane / autophagosome membrane / cell periphery / cell cortex / cytoplasmic vesicle / calmodulin binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
VTC, catalytic tunnel domain / VTC domain superfamily / Domain of unknown function DUF202 / VTC domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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)71,26913
Polymers69,5482
Non-polymers1,72211
Water6,089338
1
A: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6467
Polymers34,7741
Non-polymers8726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6236
Polymers34,7741
Non-polymers8495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.260, 100.970, 102.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 51.5 %
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→20 Å / Num. all: 46804 / Num. obs: 46804 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 35.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 7415 / Rsym value: 0.413 / % possible all: 96.9

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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: 2→19.907 Å / SU ML: 0.32 / σ(F): 0.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 2340 5.1 %RANDOM
Rwork0.2116 ---
obs0.2137 46801 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.453 Å2 / ksol: 0.349 e/Å3
Refinement stepCycle: LAST / Resolution: 2→19.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 59 338 5129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1
X-RAY DIFFRACTIONf_bond_d0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02190.39131440.29452764X-RAY DIFFRACTION94
2.0219-2.04570.36621510.2922802X-RAY DIFFRACTION97
2.0457-2.07060.36681520.28042846X-RAY DIFFRACTION97
2.0706-2.09680.31121510.272830X-RAY DIFFRACTION97
2.0968-2.12430.27861400.25722844X-RAY DIFFRACTION97
2.1243-2.15340.29141450.27042857X-RAY DIFFRACTION97
2.1534-2.18410.30361540.25222810X-RAY DIFFRACTION97
2.1841-2.21670.32791660.24862869X-RAY DIFFRACTION98
2.2167-2.25130.34241470.25392822X-RAY DIFFRACTION97
2.2513-2.28810.28811490.23092827X-RAY DIFFRACTION97
2.2881-2.32750.31031620.23082828X-RAY DIFFRACTION97
2.3275-2.36980.25791530.22842859X-RAY DIFFRACTION98
2.3698-2.41530.27211480.21832897X-RAY DIFFRACTION98
2.4153-2.46450.25051680.21742851X-RAY DIFFRACTION98
2.4645-2.5180.25031390.21522894X-RAY DIFFRACTION98
2.518-2.57650.2391610.21072829X-RAY DIFFRACTION98
2.5765-2.64070.34591360.21462875X-RAY DIFFRACTION98
2.6407-2.7120.26621590.21842861X-RAY DIFFRACTION97
2.712-2.79160.27161510.20712854X-RAY DIFFRACTION98
2.7916-2.88140.27271550.20832858X-RAY DIFFRACTION98
2.8814-2.98410.25961810.21582837X-RAY DIFFRACTION98
2.9841-3.10310.28391520.21342852X-RAY DIFFRACTION97
3.1031-3.24380.29051300.212861X-RAY DIFFRACTION97
3.2438-3.4140.22911580.19792789X-RAY DIFFRACTION96
3.414-3.62670.18231480.17982788X-RAY DIFFRACTION95
3.6267-3.90480.22421340.17872750X-RAY DIFFRACTION94
3.9048-4.29420.18261570.1722723X-RAY DIFFRACTION93
4.2942-4.90740.1838860.15972736X-RAY DIFFRACTION92
4.9074-6.15240.21911890.20432671X-RAY DIFFRACTION93
6.1524-19.90840.22851710.20782594X-RAY DIFFRACTION90

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