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Yorodumi- PDB-4d7e: An unprecedented NADPH domain conformation in Lysine Monooxygenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d7e | ||||||
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Title | An unprecedented NADPH domain conformation in Lysine Monooxygenase NbtG from Nocardia farcinica | ||||||
Components | L-LYS MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / LYSINE HYDROXYLASE / FLAVIN-DEPENDENT MONOOXYGENASES / N-HYDROXYLATING MONOOXYGENASES / SIDEROPHORE / C4A-HYDROPEROXYFLAVIN | ||||||
Function / homology | L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / L-lysine N6-monooxygenase MbtG Function and homology information | ||||||
Biological species | NOCARDIA FARCINICA IFM 10152 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Binda, C. / Robinson, R. / Keul, N. / Rodriguez, P. / Robinson, H.H. / Mattevi, A. / Sobrado, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: An Unprecedented Nadph Domain Conformation in Lysine Monooxygenase Nbtg Provides Insights Into Uncoupling of Oxygen Consumption from Substrate Hydroxylation. Authors: Binda, C. / Robinson, R.M. / Martin Del Campo, J.S. / Keul, N.D. / Rodriguez, P.J. / Robinson, H.H. / Mattevi, A. / Sobrado, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d7e.cif.gz | 584.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7e.ent.gz | 502.7 KB | Display | PDB format |
PDBx/mmJSON format | 4d7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7e ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7e | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46595.727 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOCARDIA FARCINICA IFM 10152 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP10 / References: UniProt: Q5Z1T5 #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | Sequence details | K184A MUTANT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 10% W/V PEG6000, 5% V/V 2, 4-METHYLPENTANDIOL (MPD), 0.1 M HEPES/NAOH PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.075 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→80 Å / Num. obs: 68260 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.4→91.19 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 25.517 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 70.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→91.19 Å
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Refine LS restraints |
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