+Open data
-Basic information
Entry | Database: PDB / ID: 5cet | ||||||
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Title | Crystal structure of Rv2837c | ||||||
Components | Bifunctional oligoribonuclease and PAP phosphatase NrnA | ||||||
Keywords | HYDROLASE / phosphodiesterase / c-di-AMP / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Wang, F. / He, Q. / Zhu, D. / Liu, S. / Gu, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase Authors: He, Q. / Wang, F. / Liu, S. / Zhu, D. / Cong, H. / Gao, F. / Li, B. / Wang, H. / Lin, Z. / Liao, J. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cet.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cet.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/5cet ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5cet | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 35869.820 Da / Num. of mol.: 1 / Fragment: UNP residues 10-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: nrnA, Rv2837c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P71615, Hydrolases; Acting on ester bonds, 3'(2'),5'-bisphosphate nucleotidase | ||
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#2: Chemical | #3: 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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 10% PEG10000, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22675 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rsym value: 0.084 / Net I/σ(I): 23.94 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5.19 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→37.26 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.235 Å2 / ksol: 0.336 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→37.26 Å
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Refine LS restraints |
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LS refinement shell |
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