[English] 日本語
Yorodumi- PDB-2jat: Structure of deoxyadenosine kinase from M.mycoides with products ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jat | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound | ||||||
Components | DEOXYGUANOSINE KINASE | ||||||
Keywords | TRANSFERASE / KINASE / DEOXYRIBONUCLEOSIDE KINASE | ||||||
Function / homology | Function and homology information deoxyguanosine kinase / deoxyguanosine kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | MYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Welin, M. / Wang, L. / Eriksson, S. / Eklund, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure-Function Analysis of a Bacterial Deoxyadenosine Kinase Reveals the Basis for Substrate Specificity. Authors: Welin, M. / Wang, L. / Eriksson, S. / Eklund, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jat.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jat.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 2jat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jat ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jat | HTTPS FTP |
---|
-Related structure data
Related structure data | 2jaqC 2jasSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (-0.4993, -0.8664, 0.000668), Vector: |
-Components
#1: Protein | Mass: 24288.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria) Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93IG4, deoxyguanosine kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.3 % |
---|---|
Crystal grow | pH: 5.9 / Details: 20% PEG 3350, 0.2 M MGCL2, pH 5.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2006 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43 Å / Num. obs: 11196 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JAS Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 29.663 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 68-72, 114-122 AND 143-147 ARE DISORDERED. THE DEOXYCYTIDINE PART OF DCDP IS VERY FLEXIBLE AND MODELLED AS A DIPHOSPHATE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|