- PDB-6cpt: crystal structure of yeast caPDE2 in complex with IBMX -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6cpt
Title
crystal structure of yeast caPDE2 in complex with IBMX
Components
Phosphodiesterase
Keywords
HYDROLASE / yeast phosphodiesterase-1
Function / homology
Function and homology information
Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / 3',5'-cyclic-nucleotide phosphodiesterase activity / signal transduction / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal grow
Temperature: 297 K / Method: vapor diffusion, hanging drop Details: The 10-15 mg/ml full length caPDE2 (1-571) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and crystallized at room temperature by hanging ...Details: The 10-15 mg/ml full length caPDE2 (1-571) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and crystallized at room temperature by hanging drop against a well buffer of 50 mM MES, pH 6.5, 0.1 M ammonium sulfate, 6-10% PEG8000, or a buffer of 50 mM Na citrate pH 5.6, 0.1 M ammonium acetate, 5% glycerol, and 6-10% PEG3350. The caPDE2-IBMX complex was prepared by soaking the native crystal s in the crystallization buffer with 10 mM IBMX
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2017
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.9→65.53 Å / Num. obs: 47636 / % possible obs: 97.4 % / Redundancy: 7.2 % / Net I/σ(I): 14.5
Reflection shell
Resolution: 1.9→1.93 Å
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
HKL-2000
datareduction
HKL-2000
datascaling
AMoRE
phasing
Refinement
Resolution: 1.9→65.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.224 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21294
2333
4.9 %
RANDOM
Rwork
0.18968
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obs
0.19083
45302
96.88 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å