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Yorodumi- PDB-3b1r: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b1r | ||||||
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Title | Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with AMP-Mg-AMP | ||||||
Components | Ribokinase, putative | ||||||
Keywords | TRANSFERASE / Rossmann Fold / kinase / ATP binding / Mg binding / Nucleoside binding | ||||||
Function / homology | Function and homology information phosphotransferase activity, alcohol group as acceptor / kinase activity / phosphorylation / nucleotide binding Similarity search - Function | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity Authors: Yasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b1r.cif.gz | 388.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1r.ent.gz | 313.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1r ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1r | HTTPS FTP |
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-Related structure data
Related structure data | 3b1nSC 3b1oC 3b1pC 3b1qC 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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-Components
#1: Protein | Mass: 35066.723 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1158 / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88 / References: UniProt: Q2SZE4, EC: 2.7.1.143 #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-MG / #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: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.1M Tris, 0.2M MgCl2, 20% PEG 8000, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 2, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→50 Å / Num. obs: 136213 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.7 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B1N Resolution: 2→42.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.659 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The refinement was performed using twinning operator (-H, H+K, -L) and with estimating the twinning fraction.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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