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- PDB-3g3q: Crystal structure of a eukaryotic polyphosphate polymerase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g3q | ||||||
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Title | Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer | ||||||
![]() | Vacuolar transporter chaperone 4 | ||||||
![]() | BIOSYNTHETIC PROTEIN / polyphosphate polymerase / polyphosphate kinase / VTC complex / vacuolar transporter chaperone / tunnel enzyme / Membrane / Phosphoprotein / Transmembrane / Vacuole | ||||||
Function / homology | ![]() vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / inositol hexakisphosphate binding / vacuolar transport ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / inositol hexakisphosphate binding / vacuolar transport / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hothorn, M. / Scheffzek, K. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.9 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.4 KB | Display | ![]() |
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Full document | ![]() | 478.1 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g3oSC ![]() 3g3rC ![]() 3g3tC ![]() 3g3uC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 34773.754 Da / Num. of mol.: 2 / Fragment: UNP residues 189-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: J1345, PHM3, VTC4, YJL012C / Plasmid: pETM11 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THERE 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 POLYPHOSPH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.72 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2007 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3g3o Resolution: 2.64→19.824 Å / SU ML: 0.43 / σ(F): 1.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage 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 step | Cycle: LAST / Resolution: 2.64→19.824 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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