[English] 日本語
Yorodumi- PDB-7ckj: Crystal structure of CMP kinase in complex with CMP from Thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ckj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of CMP kinase in complex with CMP from Thermus thermophilus HB8 | |||||||||
Components | Cytidylate kinase | |||||||||
Keywords | TRANSFERASE / CMP kinase / CMP complex / open conformation / nucleotide metabolism / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information (d)CMP kinase / CMP kinase activity / dCMP kinase activity / : / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: PLoS ONE / Year: 2020 Title: The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor. Authors: Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ckj.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ckj.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ckj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ckj_validation.pdf.gz | 838.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ckj_full_validation.pdf.gz | 842.6 KB | Display | |
Data in XML | 7ckj_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7ckj_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ckj ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ckj | HTTPS FTP |
-Related structure data
Related structure data | 2cmkS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22584.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: cmk, TTHA0458 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL35, (d)CMP kinase |
---|---|
#2: Chemical | ChemComp-C5P / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M BIS-TRIS, 3.5M Sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 38410 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.066 / Χ2: 1.997 / Net I/σ(I): 28 / Num. measured all: 312320 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CMK Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||
Solvent computation | Bsol: 45.9207 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 53.42 Å2 / Biso mean: 19.4958 Å2 / Biso min: 8.36 Å2
| ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→50 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.001
| ||||||||||||||||||||||||
Xplor file |
|