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Yorodumi- PDB-4rzx: Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rzx | ||||||
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Title | Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 | ||||||
Components | Probable thymidylate kinase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Biswas, A. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: To be Published Title: Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 Authors: Biswas, A. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rzx.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rzx.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rzx_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 4rzx_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 4rzx_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4rzx_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/4rzx ftp://data.pdbj.org/pub/pdb/validation_reports/rz/4rzx | HTTPS FTP |
-Related structure data
Related structure data | 2plrS S: Starting model for refinement |
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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: 24631.482 Da / Num. of mol.: 2 / Fragment: Thymidylate Kinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: Strain7 / Gene: STK_15430, tmk / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q970Q8, dTMP kinase #2: Chemical | #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | |
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-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: 44.59 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium, 15% w/v Polyethylene glycol 3,350, 0.5 M Sodium fluoride, pH 7.0, Microbatch Underoil, ...Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium, 15% w/v Polyethylene glycol 3,350, 0.5 M Sodium fluoride, pH 7.0, Microbatch Underoil, temperature 293.0K, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Details: RH Coated Bent-Cyrindrical MIRROR |
Radiation | Monochromator: SI-1 1 1 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20021 / % possible obs: 99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.348 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.66 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PLR Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.8 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.249 / 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 mean: 59.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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