[English] 日本語
Yorodumi- PDB-4wod: The duplicated taurocyamine kinase from Schistosoma mansoni compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wod | ||||||
---|---|---|---|---|---|---|---|
Title | The duplicated taurocyamine kinase from Schistosoma mansoni complexed with arginine | ||||||
Components | Taurocyamine kinase | ||||||
Keywords | TRANSFERASE / duplicated / substrate specificity / transition state | ||||||
Function / homology | Function and homology information taurocyamine kinase / taurocyamine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / oxidoreductase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Merceron, R. / Awama, A. / Montserret, R. / Marcillat, O. / Gouet, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The Substrate-free and -bound Crystal Structures of the Duplicated Taurocyamine Kinase from the Human Parasite Schistosoma mansoni. Authors: Merceron, R. / Awama, A.M. / Montserret, R. / Marcillat, O. / Gouet, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wod.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wod.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wod_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wod_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 4wod_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4wod_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/4wod ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wod | HTTPS FTP |
-Related structure data
Related structure data | 4wo8SC 4woeC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 80422.703 Da / Num. of mol.: 1 / Fragment: UNP residues 31-746 / Mutation: A11V D235G I237T D493G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_194770 / Production host: Escherichia coli (E. coli) / References: UniProt: P16641, taurocyamine kinase |
---|---|
#2: Chemical | ChemComp-ARG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 200 mM ammonium tartrate dibasic pH 5.4, 20% (w/v) polyethylene glycol 3350, 20% (v/v) ethylene glycol, 5 mM L-Arginine PH range: 5.4 - 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 58922 / Num. obs: 58275 / % possible obs: 98.9 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rsym value: 0.106 / Net I/σ(I): 12.11 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.41 / CC1/2: 0.892 / Rsym value: 0.456 / % possible all: 96.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WO8 Resolution: 1.9→45.813 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.18 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.813 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|