[English] 日本語
Yorodumi- PDB-4tlz: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-NADP+-L-orn -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tlz | ||||||
---|---|---|---|---|---|---|---|
Title | Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADox-NADP+-L-orn | ||||||
Components | KtzI | ||||||
Keywords | OXIDOREDUCTASE / hydroxylase / flavin / monooxygenase / ornithine | ||||||
Function / homology | Function and homology information L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / cellular biosynthetic process / organonitrogen compound biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Kutzneria sp. 744 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å | ||||||
Authors | Setser, J.W. / Drennan, C.L. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Crystallographic Evidence of Drastic Conformational Changes in the Active Site of a Flavin-Dependent N-Hydroxylase. Authors: Setser, J.W. / Heemstra, J.R. / Walsh, C.T. / Drennan, C.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4tlz.cif.gz | 356.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4tlz.ent.gz | 285.4 KB | Display | PDB format |
PDBx/mmJSON format | 4tlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/4tlz ftp://data.pdbj.org/pub/pdb/validation_reports/tl/4tlz | HTTPS FTP |
---|
-Related structure data
Related structure data | 4tlxC 4tm0C 4tm1C 4tm3C 4tm4C 3s5wS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49425.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kutzneria sp. 744 (bacteria) / Gene: ktzI, KUTG_08917 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8CF85 |
---|
-Non-polymers , 5 types, 606 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-ORN / #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.9-1.15 M potassium thiocyanate, 22-25% PEG 3350, 0.1 M Bis-tris propane pH 8.5 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→100 Å / Num. obs: 83380 / % possible obs: 99 % / Redundancy: 4.1 % / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.41→2.45 Å / % possible obs: 99.5 % / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.568 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S5W Resolution: 2.411→47.299 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.411→47.299 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|