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Open data
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Basic information
Entry | Database: PDB / ID: 3rl3 | ||||||
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Title | Rat metallophosphodiesterase MPPED2 | ||||||
![]() | Metallophosphoesterase MPPED2 | ||||||
![]() | HYDROLASE / alpha-beta fold / metallophosphodiesterase / wild type / GMP | ||||||
Function / homology | ![]() GMP binding / phosphoric diester hydrolase activity / AMP binding / manganese ion binding / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Podobnik, M. / Dermol, U. | ||||||
![]() | ![]() Title: Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with WAGR syndrome. Authors: Dermol, U. / Janardan, V. / Tyagi, R. / Visweswariah, S.S. / Podobnik, M. #1: Journal: J.Biol.Chem. / Year: 2009 Title: Characterization of an evolutionatily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the WAGR syndrome Authors: Tyagi, R. / Shenoy, A.R. / Visweswariah, S.S. #2: ![]() Title: A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability Authors: Podobnik, M. / Tyagi, R. / Matange, N. / Dermol, U. / Gupta, A.K. / Mattoo, R. / Seshardi, K. / Visweswariah, S.S. #3: ![]() Title: Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis Authors: Shenoy, A.R. / Capuder, M. / Draskovic, P. / Lamba, D. / Visweswariah, S.S. / Podobnik, M. #4: Journal: Biochemistry / Year: 2005 Title: The Rv0805 Gene from Mycobacterium tuberculosis Encodes a 3',5'-Cyclic Nucleotide Phosphodiesterase: Biochemical and Mutational Analysis Authors: Shenoy, A.R. / Sreenath, N. / Podobnik, M. / Kovacevic, M. / Visweswariah, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.6 KB | Display | ![]() |
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PDB format | ![]() | 107.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799 KB | Display | ![]() |
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Full document | ![]() | 799.3 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33498.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B1WBP0, Hydrolases; Acting on ester bonds |
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-Non-polymers , 5 types, 316 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / | ||||||
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#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-5GP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: MnCl2, PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2009 / Details: monochromators, mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→50 Å / Num. all: 58321 / Num. obs: 57595 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.093 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.39 Å2 / Biso mean: 18.2092 Å2 / Biso min: 8.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.454 Å / Total num. of bins used: 20
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