[English] 日本語
Yorodumi- PDB-3jq3: Crystal Structure of Lombricine Kinase, complexed with substrate ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jq3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Lombricine Kinase, complexed with substrate ADP | ||||||
Components | Lombricine kinase | ||||||
Keywords | TRANSFERASE / Mixed alpha / beta / Kinase | ||||||
Function / homology | Function and homology information phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Urechis caupo (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å | ||||||
Authors | Bush, D.J. / Kirillova, O. / Clark, S.A. / Fabiola, F. / Somasundaram, T. / Chapman, M.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The structure of lombricine kinase: implications for phosphagen kinase conformational changes. Authors: Bush, D.J. / Kirillova, O. / Clark, S.A. / Davulcu, O. / Fabiola, F. / Xie, Q. / Somasundaram, T. / Ellington, W.R. / Chapman, M.S. #1: Journal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2002 Title: Cloning and expression of a lombricine kinase from an echiuroid worm: insights into structural correlates of substrate specificity Authors: Ellington, W.R. / Bush, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3jq3.cif.gz | 162 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3jq3.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 3jq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/3jq3 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/3jq3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3jpzC 1qk1S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 40998.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Urechis caupo (invertebrata) / Plasmid: pETblue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3)pLacI / References: UniProt: Q8T6T7, EC: 2.7.3.5 |
---|---|
#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: protein at 30 mg/mL in 50mM taurocyamine, 40mM ADP & 5mM MgCl2, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 5.8, VAPOR DIFFUSION, ...Details: protein at 30 mg/mL in 50mM taurocyamine, 40mM ADP & 5mM MgCl2, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99997 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2005 / Details: double focusing mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 13213 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.122 / Χ2: 1.344 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 5.23 / Num. unique all: 1302 / Χ2: 0.456 / % possible all: 98.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model built from creatine kinase, 1qk1 Resolution: 2.503→19.994 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.34 / Isotropic thermal model: Throughout + TLS / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.974 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.73 Å2 / Biso mean: 27.429 Å2 / Biso min: 3.28 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.282 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.503→19.994 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.86 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|