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Open data
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Basic information
Entry | Database: PDB / ID: 4cy8 | ||||||
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Title | 2-hydroxybiphenyl 3-monooxygenase (HbpA) in complex with FAD | ||||||
![]() | 2-HYDROXYBIPHENYL 3-MONOOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / BIOTRANSFORMATIONS / HYDROXYLATION / FLAVIN | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jensen, C.N. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
![]() | ![]() Title: Structures of the Apo and Fad-Bound Forms of 2-Hydroxybiphenyl 3-Monooxygenase (Hbpa) Locate Activity Hotspots Identified by Using Directed Evolution. Authors: Jensen, C.N. / Mielke, T. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 445.9 KB | Display | ![]() |
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PDB format | ![]() | 358.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 92.5 KB | Display | |
Data in CIF | ![]() | 136.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cy6C ![]() 3ihgS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 63863.367 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PETYSBLIC-3C / Production host: ![]() ![]() #2: Chemical | ChemComp-FDA / #3: Water | ChemComp-HOH / | Sequence details | MUTATION T347Q IS PRESENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.7 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18% (W/V) PEG 3350, 0.15 M KSCN, 1 MM FAD IN BIS-TRIS PROPANE BUFFER AT PH 5.5, WITH A PROTEIN CONCENTRATION OF 10 MG ML-1 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91999 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→59.53 Å / Num. obs: 146673 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3IHG Resolution: 2.03→59.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.133 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 35.258 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→59.53 Å
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Refine LS restraints |
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