[English] 日本語
Yorodumi- PDB-2zoa: Malonate-bound structure of the glycerophosphodiesterase from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zoa | ||||||
---|---|---|---|---|---|---|---|
Title | Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM | ||||||
Components | Phosphohydrolase | ||||||
Keywords | HYDROLASE / MALONATE / METALLOENZYME / IRON / PHOSPHODIESTERASE | ||||||
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: 2.4 Å | ||||||
Authors | Ollis, D.L. / Jackson, C.J. / Carr, P.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Authors: Jackson, C.J. / Hadler, K.S. / Carr, P.D. / Oakley, A.J. / Yip, S. / Schenk, G. / Ollis, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zoa.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zoa.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/2zoa ftp://data.pdbj.org/pub/pdb/validation_reports/zo/2zoa | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zo9C 2dxnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 30772.646 Da / Num. of mol.: 2 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): DH5a References: UniProt: Q6XBH1, glycerophosphodiester phosphodiesterase #2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE DEPOSITORS BELIEVE THAT ALA 224 AND ASP 227 ARE CORRECT AND THAT GLU 224 AND ARG 227 IN THE ...THE DEPOSITORS | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2804 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2804 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 57620 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 45.74 Å2 / Rsym value: 0.106 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 9413 / Rsym value: 0.531 / % possible all: 98.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DXN Resolution: 2.4→24.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.786 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 45.824 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→24.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|