[English] 日本語
Yorodumi- PDB-2i7g: Crystal Structure of Monooxygenase from Agrobacterium tumefaciens -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i7g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Monooxygenase from Agrobacterium tumefaciens | ||||||
Components | Monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta / TIM barrel / helix-bundle / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å | ||||||
Authors | Kim, Y. / Xu, X. / Zheng, H. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2006 Title: The Crystal Structure of Monooxygenase from Agrobacterium tumefaciens Authors: Kim, Y. / Xu, X. / Zheng, H. / Joachimiak, A. / Edwards, A. / Savchenko, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2i7g.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2i7g.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 2i7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i7g_validation.pdf.gz | 472.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2i7g_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | 2i7g_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2i7g_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/2i7g ftp://data.pdbj.org/pub/pdb/validation_reports/i7/2i7g | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41671.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UD21, UniProt: A9CI16*PLUS #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.51 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis-tris pH 5.5, 0.2M Ammonium sulfate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97908 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Aug 22, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→29.37 Å / Num. all: 78621 / Num. obs: 78621 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2 / Num. unique all: 6883 / % possible all: 87.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.73→29.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.703 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.112 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.563 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→29.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|