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Yorodumi- PDB-3uqc: Structure of the Intracellular Kinase Homology Domain of Rv3910 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uqc | ||||||
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Title | Structure of the Intracellular Kinase Homology Domain of Rv3910 at 2.2 A resolution | ||||||
Components | PROBABLE CONSERVED TRANSMEMBRANE PROTEIN | ||||||
Keywords | TRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Kinase fold / FhaA | ||||||
Function / homology | Function and homology information lipid-linked peptidoglycan transport / lipid-linked peptidoglycan transporter activity / lipid translocation / peptidoglycan biosynthetic process / regulation of cell shape / membrane => GO:0016020 / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å | ||||||
Authors | Alber, T. / Gee, C.L. / Blair, S.R. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Sci.Signal. / Year: 2012 Title: A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria. Authors: Gee, C.L. / Papavinasasundaram, K.G. / Blair, S.R. / Baer, C.E. / Falick, A.M. / King, D.S. / Griffin, J.E. / Venghatakrishnan, H. / Zukauskas, A. / Wei, J.R. / Dhiman, R.K. / Crick, D.C. / ...Authors: Gee, C.L. / Papavinasasundaram, K.G. / Blair, S.R. / Baer, C.E. / Falick, A.M. / King, D.S. / Griffin, J.E. / Venghatakrishnan, H. / Zukauskas, A. / Wei, J.R. / Dhiman, R.K. / Crick, D.C. / Rubin, E.J. / Sassetti, C.M. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uqc.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uqc.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 3uqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/3uqc ftp://data.pdbj.org/pub/pdb/validation_reports/uq/3uqc | HTTPS FTP |
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-Related structure data
Related structure data | 3otvC 3oukSC 3ounC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30247.098 Da / Num. of mol.: 4 / Fragment: unp residues 678-963 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT4029, Rv3910 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: O05435, UniProt: P9WJK3*PLUS #2: Chemical | ChemComp-SIN / | #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: 2.03 Å3/Da / Density % sol: 39.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.7-0.8 M succinate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2008 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 2.256→47.891 Å / Num. all: 46126 / Num. obs: 46032 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.077 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.344 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3OUK Resolution: 2.256→47.877 Å / SU ML: 0.33 / Isotropic thermal model: Isotropic / σ(F): 1.89 / Phase error: 26.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.31 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.256→47.877 Å
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Refine LS restraints |
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LS refinement shell |
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