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Yorodumi- PDB-3ewc: Crystal Structure of adenosine deaminase from Plasmodial vivax in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ewc | ||||||
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Title | Crystal Structure of adenosine deaminase from Plasmodial vivax in complex with MT-coformycin | ||||||
Components | Adenosine deaminase | ||||||
Keywords | HYDROLASE / adenosine deaminase / MT-coformycin / methylthio-coformycin | ||||||
Function / homology | Function and homology information S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine deaminase activity / purine ribonucleoside monophosphate biosynthetic process / purine ribonucleoside salvage / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å | ||||||
Authors | Schramm, V.L. / Almo, S.C. / Cassera, M.B. / Ho, M.C. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and metabolic specificity of methylthiocoformycin for malarial adenosine deaminases. Authors: Ho, M.C. / Cassera, M.B. / Madrid, D.C. / Ting, L.M. / Tyler, P.C. / Kim, K. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ewc.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ewc.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ewc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/3ewc ftp://data.pdbj.org/pub/pdb/validation_reports/ew/3ewc | HTTPS FTP |
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-Related 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: 42855.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVX_111245 / Plasmid: pTrcHis2-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A5KE01, adenosine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MCF / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM NaCl, 100mM Tris, 10% PEG3350, 20% Glycerol, pH 7.5, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 26858 / % possible obs: 99.1 % / Redundancy: 5.3 % / Rsym value: 0.154 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.35 / Num. unique all: 1196 / Rsym value: 0.678 / % possible all: 92 |
-Processing
Software |
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Refinement | Resolution: 2.11→19.94 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.231 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 54.18 Å2 / Biso mean: 26.385 Å2 / Biso min: 5.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.163 Å / Total num. of bins used: 20
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