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Yorodumi- PDB-4wo8: The substrate-free duplicated taurocyamine kinase from Schistosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wo8 | ||||||
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Title | The substrate-free duplicated taurocyamine kinase from Schistosoma mansoni | ||||||
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 / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wo8.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wo8.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/4wo8 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wo8 | HTTPS FTP |
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-Related structure data
Related structure data | 4wodC 4woeC 2j1qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 200 mM ammonium tartrate dibasic pH 5.4, 20% (w/v) polyethylene glycol 3350, 20% (v/v) ethylene glycol PH range: 5.4 - 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 38515 / Num. obs: 38030 / % possible obs: 98.7 % / Redundancy: 3.1 % / Net I/σ(I): 11.71 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.11 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2j1q Resolution: 2.2→46.182 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.182 Å
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Refine LS restraints |
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LS refinement shell |
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