[English] 日本語
Yorodumi- PDB-3lkk: Crystal structure of the isopentenyl phosphate kinase substrate c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lkk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the isopentenyl phosphate kinase substrate complex | ||||||
Components | Gamma-glutamyl kinase related protein | ||||||
Keywords | TRANSFERASE / isopentenyl phosphate kinase / alternate mevalonate pathway / alpha-beta-alpha sandwich fold / substrate complex / Kinase | ||||||
Function / homology | Function and homology information isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å | ||||||
Authors | Mabanglo, M.F. / Hill, C.P. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2010 Title: X-ray structures of isopentenyl phosphate kinase. Authors: Mabanglo, M.F. / Schubert, H.L. / Chen, M. / Hill, C.P. / Poulter, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lkk.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lkk.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lkk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3lkk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3lkk_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 3lkk_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/3lkk ftp://data.pdbj.org/pub/pdb/validation_reports/lk/3lkk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27544.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: topo-cloning reaction was used to insert the Ta0103 gene, and translated protein contained histidine tag, V5 epitope and TEV protease recognition site Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: Ta0103 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: Q9HLX1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
---|---|
Crystal grow | Temperature: 274 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M MIB buffer (2:3:3 molar ratio of sodium malonate, imidazole, boric acid), pH 7.0, 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 274K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2008 / Details: mirrors |
Radiation | Monochromator: Verimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 31502 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / % possible all: 95.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T.acidophilum isopentenyl phosphate kinase solved by single-wavelength anomalous diffraction (SAD) Resolution: 2.001→29.303 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.151 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→29.303 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|