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Yorodumi- PDB-5xb2: ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xb2 | ||||||
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Title | ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5 | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / Kinase / Tranferase / Complex / Nucleotide Binding | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 Å | ||||||
Authors | Biswas, A. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate Authors: Biswas, A. / Shukla, A. / Chaudhary, S.K. / Santhosh, R. / 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 | 5xb2.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xb2.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/5xb2 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/5xb2 | HTTPS FTP |
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-Related structure data
Related structure data | 4s2eC 4s35C 5h56C 5h5bC 5h5kC 5xaiC 5xb3C 5xb5C 5xbhC 2pbrS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 22402.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: tmk, aq_969 / Production host: Escherichia coli (E. coli) / References: UniProt: O67099, dTMP kinase |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: 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: 2.57 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97372 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→54 Å / Num. obs: 23220 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.16→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3080 / CC1/2: 0.64 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PBR Resolution: 2.161→49.944 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.161→49.944 Å
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Refine LS restraints |
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LS refinement shell |
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