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Yorodumi- PDB-3k4o: Crystal Structure of Isopentenyl Phosphate Kinase from Methanocal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k4o | ||||||
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Title | Crystal Structure of Isopentenyl Phosphate Kinase from Methanocaldococcus jannaschii | ||||||
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 / SAD / Resolution: 2.05 Å | ||||||
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 | 3k4o.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k4o.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k4o_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 3k4o_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 3k4o_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3k4o_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4o ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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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: 2.78 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.6M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K |
-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: Jul 12, 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→50 Å / Num. all: 45927 / Num. obs: 45753 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.36 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.54 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 6.36 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.07 / Num. unique all: 7299 / % possible all: 98.3 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / σ(F): 0
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Solvent computation | Bsol: 64.48 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.64 Å2 / Biso mean: 41.29 Å2 / Biso min: 17.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.07 Å
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Xplor file |
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