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Yorodumi- PDB-4xwa: TMK from S.aureus in complex with the Piperidinyl Thymine class i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xwa | ||||||
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Title | TMK from S.aureus in complex with the Piperidinyl Thymine class inhibitor with a C5 ethyl-amine | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / TMK / kinase / antibacterial / piperidine / thymidine | ||||||
Function / homology | Function and homology information dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Olivier, N.B. | ||||||
Citation | Journal: Bioorg Med Chem Lett / Year: 2015 Title: A highly potent antibacterial inhibitor of Gram-positive bacterial thymidylate kinase (TMK): SAR of piperidinyl thymines at position C5 and L1 Authors: Guler, S.Y. / Martinez-Botella, G. / Breen, J. / Kawatkar, S. / Loch, J. / Olivier, N.B. / Wang, H. / Keating, T. / Otterson, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xwa.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xwa.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/4xwa ftp://data.pdbj.org/pub/pdb/validation_reports/xw/4xwa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 23454.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria) Gene: tmk, SAHV_0479 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7WYM2, dTMP kinase #2: Chemical | #3: 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: 2.19 Å3/Da / Density % sol: 43.73 % / Description: bars |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM ...Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 mM Mg2Cl using 1:1 protein:reservoir solution with the protein solution at 13 mg/mL. Crystals were harvested and soaked overnight in a solution containing 100 mM PCPT, 35% PEG 3350, 200 mM Mg2Cl and 1-2 mM TK-666 from a 100 mM DMSO stock. After soaking the crystals were cryoprotected by soaking for 15 minutes in compound-soak solution supplemented with 20% ethylene glycol. Cryoprotected crystals were mounted on nylon loops and flash-cooled in liquid nitrogen. PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 6, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.887→33.831 Å / Num. all: 31072 / Num. obs: 31072 / % possible obs: 95.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 23.81 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Rsym value: 0.037 / Net I/av σ(I): 15.813 / Net I/σ(I): 16.2 / Num. measured all: 88375 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo-state structure Resolution: 1.89→33.83 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9136 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.148
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Displacement parameters | Biso max: 114.56 Å2 / Biso mean: 27.39 Å2 / Biso min: 9.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.228 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→33.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.95 Å / Total num. of bins used: 16
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