+Open data
-Basic information
Entry | Database: PDB / ID: 1rwl | ||||||
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Title | Extracellular domain of Mycobacterium tuberculosis PknD | ||||||
Components | Serine/threonine-protein kinase pknD | ||||||
Keywords | TRANSFERASE / beta propeller / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / cellular response to phosphate starvation / positive regulation of catalytic activity / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / membrane => GO:0016020 / non-specific serine/threonine protein kinase ...negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / cellular response to phosphate starvation / positive regulation of catalytic activity / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Good, M.C. / Greenstein, A.E. / Young, T.A. / Ng, H.L. / Alber, T. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Sensor Domain of the Mycobacterium tuberculosis Receptor Ser/Thr Protein Kinase, PknD, forms a Highly Symmetric beta Propeller. Authors: Good, M.C. / Greenstein, A.E. / Young, T.A. / Ng, H.L. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwl.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwl.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwl ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwl | HTTPS FTP |
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-Related structure data
Related structure data | 1rwiSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is the monomer |
-Components
#1: Protein | Mass: 28519.459 Da / Num. of mol.: 1 / Fragment: residues 403-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PKND, RV0931C, MT0958, MTCY08C9.08 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + References: UniProt: O05871, UniProt: P9WI79*PLUS, EC: 2.7.1.37 | ||
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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 5.62 Å3/Da / Density % sol: 77.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium acetate, HEPES, cadmium sulfate, p-chloromercurybenzene sulfonic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0719 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 27, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0719 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 17505 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RWI Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.985 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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