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- PDB-3k4y: 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: 3k4y | ||||||
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Title | Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP | ||||||
![]() | isopentenyl phosphate kinase | ||||||
![]() | TRANSFERASE / small molecule kinase / ATP-binding / Methanocaldococcus jannaschii / isopentenyl monophosphate / isopentenyl diphosphate / isoprenoid biosynthesis / mevalonate pathway / archaea | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / terpenoid biosynthetic process / kinase activity / 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 | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: crystals were grown in 1.6M ammonium sulfate and then transferred to a solution containing 1.6M ammonium sulfate, 10mM IPP, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-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: 2.54→50 Å / Num. all: 22954 / Num. obs: 22723 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.87 % / Biso Wilson estimate: 47.429 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.32 |
Reflection shell | Resolution: 2.54→2.64 Å / Redundancy: 5.66 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 12156 / Num. unique all: 3643 / Num. unique obs: 2215 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: CNS rigid body / Resolution: 2.54→43.71 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.777 / SU B: 11.679 / SU ML: 0.256 / SU R Cruickshank DPI: 0.559 / SU Rfree: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.331 / 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: 104.29 Å2 / Biso mean: 42.056 Å2 / Biso min: 14.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→43.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.543→2.609 Å / Total num. of bins used: 20
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