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Yorodumi- PDB-3ork: Mycobacterium tuberculosis PknB kinase domain L33D mutant (crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ork | ||||||
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Title | Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 2) | ||||||
Components | Serine/threonine protein kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Kinase domain / Signal transduction | ||||||
Function / homology | Function and homology information regulation of cellular biosynthetic process / regulation of primary metabolic process / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Echols, N. / Lombana, T.N. / Thomsen, N.D. / Ng, H.-L. / Alber, T. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Structure / Year: 2010 Title: Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr kinase, PknB Authors: Lombana, T.N. / Echols, N. / Good, M.C. / Thomsen, N.D. / Ng, H.-L. / Greenstein, A.E. / Falick, A.M. / King, D.S. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ork.cif.gz | 141.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ork.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ork.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ork_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3ork_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ork_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3ork_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/3ork ftp://data.pdbj.org/pub/pdb/validation_reports/or/3ork | HTTPS FTP |
-Related structure data
Related structure data | 3orlC 3orpC 3ortC 1mruS 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, 1 molecules A
#1: Protein | Mass: 33520.605 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 1 to 308) / Mutation: L33D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MRA_0016, pknB, PknB (Rv0014c) / Production host: Escherichia coli (E. coli) / References: UniProt: A5TY84 |
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-Non-polymers , 5 types, 356 molecules
#2: Chemical | ChemComp-AGS / |
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#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-TRS / |
#6: 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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: 27% PEG 3350, 100mM Tris pH 8.5, 200mM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2004 |
Radiation | Monochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 41724 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.4 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MRU Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.799 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.075 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.178 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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