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- PDB-1t8q: Structural genomics, Crystal structure of Glycerophosphoryl diest... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t8q | ||||||
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Title | Structural genomics, Crystal structure of Glycerophosphoryl diester phosphodiesterase from E. coli | ||||||
![]() | Glycerophosphoryl diester phosphodiesterase, periplasmic | ||||||
![]() | HYDROLASE / Phosphodiesterase / Structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / glycerol metabolic process / vacuole / lipid metabolic process / periplasmic space / calcium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Kim, Y. / Dementieva, I. / Duke, N. / Stols, L. / Donnelly, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of Glycerophosphoryl diester phosphodiesterase from E. coli Authors: Zhang, R. / Kim, Y. / Dementieva, I. / Duke, N. / Stols, L. / Donnelly, M. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.9 KB | Display | ![]() |
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PDB format | ![]() | 248.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 506.4 KB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 91.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | This protein existed as dimer. MolA & MolD, MolB & MolC represent two dimers in the asymmetric unit. |
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Components
#1: Protein | Mass: 38944.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P09394, glycerophosphodiester phosphodiesterase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.958 Å3/Da / Density % sol: 56.8 % / Description: Friedel pairs were used |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG8000, 20% glycerol, 80 nM Na Cacodylate buffer, 0.16M Mg Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 19, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 239258 / Num. obs: 226817 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 5.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.83 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.68 / Num. unique all: 23943 / % possible all: 63.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5213 Å2 / ksol: 0.343282 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→43.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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