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Yorodumi- PDB-3d03: 1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d03 | ||||||
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Title | 1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes | ||||||
Components | Phosphohydrolase | ||||||
Keywords | HYDROLASE / glycerophosphodiesterase / metallohydrolase / phosphatase / metal ion | ||||||
Function / homology | Function and homology information glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / glycerol metabolic process / 3',5'-cyclic-AMP phosphodiesterase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacter aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hadler, K.S. / Tanifum, E. / Yip, S.H.-C. / Miti, N. / Guddat, L.W. / Jackson, C.J. / Gahan, L.R. / Carr, P.D. / Nguyen, K. / Ollis, D.L. ...Hadler, K.S. / Tanifum, E. / Yip, S.H.-C. / Miti, N. / Guddat, L.W. / Jackson, C.J. / Gahan, L.R. / Carr, P.D. / Nguyen, K. / Ollis, D.L. / Hengge, A.C. / Larrabee, J.A. / Schenk, G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes. Authors: Hadler, K.S. / Tanifum, E.A. / Yip, S.H. / Mitic, N. / Guddat, L.W. / Jackson, C.J. / Gahan, L.R. / Nguyen, K. / Carr, P.D. / Ollis, D.L. / Hengge, A.C. / Larrabee, J.A. / Schenk, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d03.cif.gz | 332.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d03.ent.gz | 271.2 KB | Display | PDB format |
PDBx/mmJSON format | 3d03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/3d03 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d03 | HTTPS FTP |
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-Related structure data
Related structure data | 2dxlS 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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-Components
#1: Protein | Mass: 30772.646 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: GPDQ / Plasmid: PCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA References: UniProt: Q6XBH1, glycerophosphodiester phosphodiesterase #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | Sequence details | ERROR INTRODUCED | |
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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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 60% Tacsimate, 100mM bis-tris, pH 7.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95367 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2007 |
Radiation | Monochromator: double crystal, second crystal sagitally focussed Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95367 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.3 Å / Num. all: 163812 / Num. obs: 163812 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.613 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DXL Resolution: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.658 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.215 Å2
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Refine analyze | Luzzati coordinate error obs: 0.232 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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