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Open data
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Basic information
Entry | Database: PDB / ID: 4cy6 | ||||||
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Title | apo structure of 2-hydroxybiphenyl 3-monooxygenase HbpA | ||||||
![]() | 2-HYDROXYBIPHENYL-3-MONOOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / FAD / HYDROXYLATION / FLAVIN / NADH | ||||||
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 | ![]() | 407.7 KB | Display | ![]() |
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PDB format | ![]() | 330.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
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Full document | ![]() | 476.1 KB | Display | |
Data in XML | ![]() | 73.1 KB | Display | |
Data in CIF | ![]() | 101.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cy8C ![]() 3ihgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.5 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18% (W/V) PEG 3350, 0.15 M KSCN 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 6M / Detector: PIXEL / Date: Dec 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→85.97 Å / Num. obs: 59321 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.76→2.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3IHG Resolution: 2.76→85.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.938 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / 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: 59.665 Å2
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Refinement step | Cycle: LAST / Resolution: 2.76→85.97 Å
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Refine LS restraints |
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