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Yorodumi- PDB-5xnx: Crystallographic structure of the enzymatically active N-terminal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xnx | ||||||
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Title | Crystallographic structure of the enzymatically active N-terminal domain of the Rel protein from Mycobacterium tuberculosis | ||||||
Components | Bifunctional (p)ppGpp synthase/hydrolase RelA | ||||||
Keywords | HYDROLASE / TRANSFERASE / RelA / Mycobacterium tuberculosis / HD DOMAIN / HELIX BUNDLE / Synthetase domain / (p)ppGpp / Stringent response | ||||||
Function / homology | Function and homology information guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / stringent response / peptidoglycan-based cell wall / manganese ion binding / kinase activity / phosphorylation ...guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / stringent response / peptidoglycan-based cell wall / manganese ion binding / kinase activity / phosphorylation / GTP binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Singal, B. / Balakrishna, A.M. / Manimekalai, M.S.S. / Nartey, W. / Gruber, G. | ||||||
Citation | Journal: FEBS Lett. / Year: 2017 Title: Crystallographic and solution structure of the N-terminal domain of the Rel protein from Mycobacterium tuberculosis Authors: Singal, B. / Balakrishna, A.M. / Nartey, W. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xnx.cif.gz | 485.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xnx.ent.gz | 402.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xnx ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xnx | HTTPS FTP |
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-Related structure data
Related structure data | 1vj7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 14 - 344 / Label seq-ID: 14 - 344
NCS oper:
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-Components
#1: Protein | Mass: 44651.188 Da / Num. of mol.: 4 / Fragment: UNP residues 1-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: relA, Rv2583c, MTCY227.18 / Plasmid: pET9D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P9WHG9, GTP diphosphokinase, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase #2: Chemical | |
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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: 3.19 Å3/Da / Density % sol: 61.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.8M succinic acid, pH 7.0, 0.2M MgCl2, 0.2-0.4M Trimethylamin-N-oxide, 20% w/v Benzamidine hydrochloride hydrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2017 / Details: mirrors | |||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.7→20 Å / Num. obs: 23372 / % possible obs: 99.2 % / Redundancy: 11.1 % / CC1/2: 0.9874 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.9 / CC1/2: 0.962 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vj7 Resolution: 3.7→10.02 Å / Cor.coef. Fo:Fc: 0.741 / Cor.coef. Fo:Fc free: 0.733 / SU B: 112.217 / SU ML: 0.771 / Cross valid method: THROUGHOUT / ESU R Free: 0.2 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.249 Å2
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Refinement step | Cycle: 1 / Resolution: 3.7→10.02 Å
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Refine LS restraints |
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