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- PDB-3k56: Crystal Structure of Isopentenyl Phosphate Kinase from M. jannasc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k56 | ||||||
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Title | Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP beta-S | ||||||
![]() | isopentenyl phosphate kinase | ||||||
![]() | TRANSFERASE / small molecule kinase / ATP-binding / ATP gamma-S / Methanocaldococcus jannaschii / isopentenyl monophosphate / isopentenyl diphosphate / isoprenoid biosynthesis / mevalonate pathway / archaea | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / terpenoid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dellas, N. / Noel, J.P. | ||||||
![]() | ![]() Title: Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates. Authors: Dellas, N. / Noel, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1005.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k4oSC ![]() 3k4yC ![]() 3k52C 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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Unit cell |
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Components
#1: Protein | Mass: 30009.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ0044 / Plasmid: pHIS8 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.6M ammonium sulfate, 5mM ATP gamma-S, 1mM IP, 2mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2008 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. all: 29535 / Num. obs: 29290 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.01 % / Biso Wilson estimate: 57.911 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.65 |
Reflection shell | Resolution: 2.34→2.44 Å / Redundancy: 6.76 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3 / Num. measured obs: 20588 / Num. unique all: 4681 / Num. unique obs: 3160 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 3K4O Resolution: 2.34→42.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.786 / SU B: 8.419 / SU ML: 0.196 / SU R Cruickshank DPI: 0.325 / SU Rfree: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.31 Å2 / Biso mean: 51.764 Å2 / Biso min: 17.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→42.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.405 Å / Total num. of bins used: 20
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