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Yorodumi- PDB-4b65: A. fumigatus ornithine hydroxylase (SidA), reduced state bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b65 | ||||||
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Title | A. fumigatus ornithine hydroxylase (SidA), reduced state bound to NADP(H) | ||||||
Components | L-ORNITHINE N5 MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / SIDEROPHORE / FLAVIN | ||||||
Function / homology | Function and homology information L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / secondary metabolite biosynthetic process / NADP+ binding ...L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / secondary metabolite biosynthetic process / NADP+ binding / monooxygenase activity / intracellular iron ion homeostasis / iron ion binding Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Franceschini, S. / Fedkenheuer, M. / Vogelaar, N.J. / Robinson, H.H. / Sobrado, P. / Mattevi, A. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural Insight Into the Mechanism of Oxygen Activation and Substrate Selectivity of Flavin-Dependent N-Hydroxylating Monooxygenases. Authors: Franceschini, S. / Fedkenheuer, M. / Vogelaar, N.J. / Robinson, H.H. / Sobrado, P. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b65.cif.gz | 200.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b65.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 4b65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b65_validation.pdf.gz | 982.7 KB | Display | wwPDB validaton report |
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Full document | 4b65_full_validation.pdf.gz | 988 KB | Display | |
Data in XML | 4b65_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4b65_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b65 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b65 | HTTPS FTP |
-Related structure data
Related structure data | 4b63SC 4b64C 4b66C 4b67C 4b68C 4b69C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56959.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SE95, UniProt: E9QYP0*PLUS |
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-Non-polymers , 5 types, 201 molecules
#2: Chemical | ChemComp-FAD / | ||
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#3: Chemical | ChemComp-NDP / | ||
#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.6 Details: HANGING DROP VAPOR DIFFUSION METHOD, WITH A RESERVOIR SOLUTION CONTAINING; 1.6 M AMMONIUM SULFATE, 0.1 M HEPES, 2% DIOXANE, PH 6.6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 21091 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B63 Resolution: 2.32→72.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.261 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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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: 24.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→72.81 Å
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Refine LS restraints |
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