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Yorodumi- PDB-3b1p: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b1p | ||||||
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Title | Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-inosine | ||||||
Components | Ribokinase, putative | ||||||
Keywords | TRANSFERASE / Rossmann Fold / kinase / ATP binding / Mg binding / Nucleoside binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 3b1p.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1p.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 3b1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b1p_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3b1p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3b1p_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3b1p_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1p ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1p | HTTPS FTP |
-Related structure data
Related structure data | 3b1nSC 3b1oC 3b1qC 3b1rC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35751.480 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-NOS / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 0.1M Na citrate, 16% PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2009 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 37278 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5.3 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B1N Resolution: 1.7→44.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.009 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / 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: 20.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→44.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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