[English] 日本語
Yorodumi- PDB-2zo9: Malonate-bound structure of the glycerophosphodiesterase from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zo9 | ||||||
---|---|---|---|---|---|---|---|
Title | Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference | ||||||
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: 2.2 Å | ||||||
Authors | Jackson, C.J. / Carr, P.D. / Ollis, D.L. | ||||||
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 | 2zo9.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zo9.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/2zo9 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/2zo9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zoaC 2dxnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7, VAPOR DIFFUSION, temperature 277K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2947 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: 1.2947 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 73371 / % possible obs: 98.2 % / Observed criterion σ(I): 20.9 / Biso Wilson estimate: 50.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 11622 / Rsym value: 0.474 / % possible all: 94.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DXN Resolution: 2.2→29.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.812 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / 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: 50.636 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|