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Yorodumi- PDB-3k52: Crystal Structure of Isopentenyl Phosphate Kinase from M. jannasc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k52 | ||||||
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Title | Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP | ||||||
Components | isopentenyl phosphate kinase | ||||||
Keywords | TRANSFERASE / small molecule kinase / ATP-binding / Methanocaldococcus jannaschii / isopentenyl monophosphate / isopentenyl diphosphate / isoprenoid biosynthesis / mevalonate pathway / archaea | ||||||
Function / homology | Function and homology information isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / terpenoid biosynthetic process / kinase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Model details | Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP | ||||||
Authors | Dellas, N. / Noel, J.P. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k52.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k52.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k52_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 3k52_full_validation.pdf.gz | 499 KB | Display | |
Data in XML | 3k52_validation.xml.gz | 25 KB | Display | |
Data in CIF | 3k52_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k52 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k52 | HTTPS FTP |
-Related structure data
-Links
-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.) Methanocaldococcus jannaschii (archaea) Gene: MJ0044 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60352 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: crystals were grown in 1.6M ammonium sulfate, transferred to 1.6M ammonium sulfate, 2mM IP, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
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: 2.7→50 Å / Num. all: 19488 / Num. obs: 19309 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.88 % / Biso Wilson estimate: 54.186 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.53 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.81 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 10240 / Num. unique all: 3076 / Num. unique obs: 1818 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.65 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.796 / SU B: 13.182 / SU ML: 0.277 / SU R Cruickshank DPI: 1.029 / SU Rfree: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.029 / ESU R Free: 0.377 / 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: 91.43 Å2 / Biso mean: 48.71 Å2 / Biso min: 18.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.771 Å / Total num. of bins used: 20
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