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Yorodumi- PDB-5den: The First Structure of a Full-Length Mammalian Phenylalanine Hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5den | ||||||
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Title | The First Structure of a Full-Length Mammalian Phenylalanine Hydroxylase Reveals the Architecture of an Auto-inhibited Tetramer | ||||||
Components | Phenylalanine-4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / mammalian phenylalanine hydroxylase / allosteric regulation by phenylalanine / phenylketonuria / ACT-containing | ||||||
Function / homology | Function and homology information tyrosine biosynthetic process, by oxidation of phenylalanine / Phenylalanine metabolism / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / L-phenylalanine catabolic process / amino acid binding / iron ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Arturo, E.C. / Loll, P.J. / Jaffe, E.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer. Authors: Arturo, E.C. / Gupta, K. / Heroux, A. / Stith, L. / Cross, P.J. / Parker, E.J. / Loll, P.J. / Jaffe, E.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5den.cif.gz | 687.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5den.ent.gz | 579.9 KB | Display | PDB format |
PDBx/mmJSON format | 5den.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5den ftp://data.pdbj.org/pub/pdb/validation_reports/de/5den | HTTPS FTP |
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-Related structure data
Related structure data | 1phzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 51871.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pah / Production host: Escherichia coli (E. coli) / References: UniProt: P04176, phenylalanine 4-monooxygenase #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein was stored at -80C, then thawed in a water bath at 25C for ~ 20 minutes. The protein, at a concentration of 9.5 mg/mL was diluted to 5.5 mg/mL using 30 mM Tris pH 7.4, 116 mM KCl, ...Details: Protein was stored at -80C, then thawed in a water bath at 25C for ~ 20 minutes. The protein, at a concentration of 9.5 mg/mL was diluted to 5.5 mg/mL using 30 mM Tris pH 7.4, 116 mM KCl, 15% glycerol. The diluted protein was left at 4C for ~ hours, then at room temperature for ~ 20 minutes prior to preparation of the crystallization tray. The 2 uL hanging drop (containing 1:1 protein:reservoir) hung over a reservoir solution containing 140 mM Na-acetate, 70 mM Na-citrate, 100 mM Na-cacodylate (pH 6.5), and 31.5% PEG 1,000 (Hampton Research). Temp details: Temperature is approximate. Temperature maintenance was passive; crystal trays were stored in an incubator that remained off. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→38.1 Å / Num. obs: 38661 / % possible obs: 91.01 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.06 |
Reflection shell | Resolution: 2.9→3.004 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.56 / % possible all: 76.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PHZ Resolution: 2.9→38.1 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.95 Å2 / Biso mean: 81.3783 Å2 / Biso min: 29.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→38.1 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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