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- PDB-3tk2: Crystallographic structure of phenylalanine hydroxylase from Chro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tk2 | ||||||
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Title | Crystallographic structure of phenylalanine hydroxylase from Chromobacterium violaceum cocrystallized with phenylalanine in a site distal to the active site | ||||||
![]() | Phenylalanine-4-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Protein-Substate complex / Mixed alpha / beta / Hydroxylase / Phenylalanine / Tetrahydrobiopterin / Iron (II) / Molecular oxygen / Hydroxylation | ||||||
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: An additional substrate binding site in a bacterial phenylalanine hydroxylase. Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Corn, I.R. / Wagner, K.T. / 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 | ![]() | 139.1 KB | Display | ![]() |
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PDB format | ![]() | 106.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.8 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tcyC ![]() 3tk4C ![]() 4esmC ![]() 4etlC ![]() 4jpxC ![]() 4jpyC ![]() 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: 34061.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-PHE / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 0.005M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, 0.1M hexammine cobalt (II) chloride, 1.0M guanidine hydrochloride, pH 7.0, ...Details: 0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 0.005M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, 0.1M hexammine cobalt (II) chloride, 1.0M guanidine hydrochloride, pH 7.0, 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: Jun 26, 2011 |
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: 50401 / Num. obs: 47843 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.35→1.37 Å / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LTU Resolution: 1.35→24.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.998 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R Free: 0.067 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→24.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.386 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.7562 Å / Origin y: 0.0595 Å / Origin z: -0.3089 Å
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