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Yorodumi- PDB-4tm0: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-ox-NADP+-L-orn -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tm0 | ||||||
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Title | Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-ox-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: 2.74 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tm0.cif.gz | 346.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tm0.ent.gz | 277.3 KB | Display | PDB format |
PDBx/mmJSON format | 4tm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/4tm0 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/4tm0 | HTTPS FTP |
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-Related structure data
Related structure data | 4tlxC 4tlzC 4tm1C 4tm3C 4tm4C 3s5wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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-Non-polymers , 5 types, 259 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-ORN / #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→100 Å / Num. obs: 57847 / % possible obs: 97.9 % / Redundancy: 4.5 % / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.74→2.79 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.567 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S5W Resolution: 2.74→47.158 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→47.158 Å
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Refine LS restraints |
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LS refinement shell |
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