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- PDB-4q3z: Crystal structure of C. violaceum phenylalanine hydroxylase D139K... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q3z | ||||||
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Title | Crystal structure of C. violaceum phenylalanine hydroxylase D139K mutation | ||||||
![]() | Phenylalanine-4-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Mutation / hydroxylase / phenylalanine hydroxylase / kinetics / metals / Chromobacterium / phenylketonuria / biopterin / Mixed alpha helix-beta sheet | ||||||
Function / homology | ![]() phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-phenylalanine catabolic process / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ronau, J.A. / Abu-Omar, M.M. / Das, C. | ||||||
![]() | ![]() Title: A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis. Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Liedl, K.R. / Abu-Omar, M.M. / Das, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.1 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 426.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4q3wC ![]() 4q3xC ![]() 4q3yC ![]() 1ltuS 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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Unit cell |
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Components
#1: Protein | Mass: 33661.109 Da / Num. of mol.: 1 / Mutation: D139K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: phhA, CV_3180 / Plasmid: pET3a / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Na-HEPES pH 7.0, 10 mM Magnesium chloride hexahydrate, 5 mM Nickel(II) chloride hexahydrate, 15% w/v polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2012 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 50858 / Num. obs: 48519 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.35→1.37 Å / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1LTU Resolution: 1.35→21.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.163 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 17.757 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→21.81 Å
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Refine LS restraints |
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