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- PDB-2xls: Joint-functions of protein residues and NADP(H) in oxygen-activat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xls | ||||||
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Title | Joint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: Asn78Lys mutant | ||||||
![]() | FLAVIN-CONTAINING MONOOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / TRIMETHYAMINURIA | ||||||
Function / homology | ![]() trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orru, R. / Fraaije, M.W. / Mattevi, A. | ||||||
![]() | ![]() Title: Joint-Functions of Protein Residues and Nadp(H) in Oxygen-Activation by Flavin-Containing Monooxygenase Authors: Orru, R. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.4 KB | Display | ![]() |
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PDB format | ![]() | 306.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xlpC ![]() 2xlrC ![]() 2xltC ![]() 2xluC ![]() 2vq7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: NAP / End label comp-ID: NAP / Refine code: 1 / Auth seq-ID: 7 - 501 / Label seq-ID: 7
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53355.832 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SK1 / Plasmid: PET28 / Production host: ![]() ![]() References: UniProt: Q83XK4, flavin-containing monooxygenase |
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-Non-polymers , 5 types, 40 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 73 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASN 73 TO LYS ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.31 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 7.5 Details: CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), ...Details: CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), AND 20% (W/V) PEG4000 IN 100 MM NA/HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 3→50 Å / Num. obs: 72308 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VQ7 Resolution: 3→95.17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.945 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 32.9 Å2
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Refinement step | Cycle: LAST / Resolution: 3→95.17 Å
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Refine LS restraints |
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