[English] 日本語
Yorodumi- PDB-1wkk: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wkk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP | ||||||
Components | nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / nucleoside diphosphate kinase / complex with GDP / Thermus themophilus HB8 / kinase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 Authors: Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wkk.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wkk.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1wkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wkk_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wkk_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 1wkk_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 1wkk_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkk ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkk | HTTPS FTP |
-Related structure data
Related structure data | 1wkjSC 1wklC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y+1, x-y+1, z and -x+y, -x+1, z. |
-Components
#1: Protein | Mass: 15366.903 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ndk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLV5, nucleoside-diphosphate kinase #2: Chemical | ChemComp-GDP / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 13% PEG4000, 0.09M Ammonium Acetate, 15% Glycerol, 0.1M Sodium Citrate, 0.001M GTP, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 2, 2003 |
Radiation | 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. obs: 161023 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 16.2 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WKJ Resolution: 2.7→50 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|