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Yorodumi- PDB-4rfv: Structure of the Mycobacterium tuberculosis APS kinase CysC Cys55... -
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-Basic information
Entry | Database: PDB / ID: 4rfv | ||||||
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Title | Structure of the Mycobacterium tuberculosis APS kinase CysC Cys556Ala mutant | ||||||
Components | Bifunctional enzyme CysN/CysC | ||||||
Keywords | TRANSFERASE / APS kinase domain / inactive mutant / sulfur assimilation / cysteine biosynthesis / redox regulation | ||||||
Function / homology | Function and homology information sulfate adenylyltransferase complex (ATP) / cellular response to sulfur starvation / Sulfate assimilation / sulfate assimilation via adenylyl sulfate reduction / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / translation elongation factor activity ...sulfate adenylyltransferase complex (ATP) / cellular response to sulfur starvation / Sulfate assimilation / sulfate assimilation via adenylyl sulfate reduction / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / translation elongation factor activity / cellular response to oxidative stress / phosphorylation / GTPase activity / GTP binding / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Poyraz, O. / Brunner, K. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis. Authors: Poyraz, O. / Brunner, K. / Lohkamp, B. / Axelsson, H. / Hammarstrom, L.G. / Schnell, R. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rfv.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rfv.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/4rfv ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rfv | HTTPS FTP |
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-Related structure data
Related structure data | 4bzpSC 4bzqC 4bzxC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21278.084 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 424-612) / Mutation: C556S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: cysN, cysNC, MTCY373.05, Rv1286 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P9WNM5, sulfate adenylyltransferase, adenylyl-sulfate kinase #2: Chemical | ChemComp-PO4 / | #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 grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 21% PEG 3350, 0.2M ammonium nitrate, 5mM magnesium chloride, 5mM ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91842 Å | |||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014 / Details: mirrors | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.69→59.28 Å / Num. all: 32714 / Num. obs: 32681 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 13.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4BZP Resolution: 1.69→59.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.436 / SU ML: 0.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R: 0.109 / ESU R Free: 0.108 / 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: 24.155 Å2
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Refine analyze | Luzzati sigma a obs: 0.108 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→59.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Total num. of bins used: 20
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