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Yorodumi- PDB-5h5k: ATP and CMP bound Crystal structure of thymidylate kinase (aq_969... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h5k | ||||||
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Title | ATP and CMP 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 / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 5h5k.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h5k.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h5k_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5h5k_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5h5k_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5h5k_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/5h5k ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h5k | HTTPS FTP |
-Related structure data
Related structure data | 4s2eC 4s35C 5h56C 5h5bC 5xaiC 5xb2C 5xb3C 5xb5C 5xbhC 2pbrS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#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, 72 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 18641 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 6.83 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.21 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PBR Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.395 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.252 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.468 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→30 Å
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Refine LS restraints |
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