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Yorodumi- PDB-6n1k: Full-length human phenylalanine hydroxylase (PAH) in the resting state -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n1k | ||||||
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Title | Full-length human phenylalanine hydroxylase (PAH) in the resting state | ||||||
Components | Phenylalanine-4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / resting-state PAH / allosterically controlled aromatic amino acid hydroxylase | ||||||
Function / homology | Function and homology information Phenylketonuria / Phenylalanine metabolism / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / catecholamine biosynthetic process / L-phenylalanine catabolic process / amino acid biosynthetic process / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.057 Å | ||||||
Authors | Arturo, E.C. / Jaffe, E.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. Authors: Arturo, E.C. / Gupta, K. / Hansen, M.R. / Borne, E. / 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 | 6n1k.cif.gz | 979 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n1k.ent.gz | 844.3 KB | Display | PDB format |
PDBx/mmJSON format | 6n1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n1k_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 6n1k_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 6n1k_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 6n1k_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/6n1k ftp://data.pdbj.org/pub/pdb/validation_reports/n1/6n1k | HTTPS FTP |
-Related structure data
Related structure data | 1j8uS 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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-Components
#1: Protein | Mass: 51781.648 Da / Num. of mol.: 4 / Mutation: C29S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-FE / #4: 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: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: hPAH C29S was obtained from of the 6His-SUMO fusion using a sodium phosphate buffer. Crystals were grown from C29S (16 mg/mL) in 2 mM Tris-HCl pH 7.4, mixed with reservoir solutions in a ...Details: hPAH C29S was obtained from of the 6His-SUMO fusion using a sodium phosphate buffer. Crystals were grown from C29S (16 mg/mL) in 2 mM Tris-HCl pH 7.4, mixed with reservoir solutions in a protein:reservoir ratio equal to 1:1.25 and equilibrated using hanging drop vapor diffusion. The 1 mL reservoir solution initially contained 16% PEG 3350, 100 mM bis-tris-propane pH 7.5 and 200 mM sodium sulfate. Crystals appeared at 295K within one day in the dark. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.008 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→37 Å / Num. obs: 39316 / % possible obs: 99.54 % / Redundancy: 3.9 % / Biso Wilson estimate: 93.6345104659 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0783 / Rrim(I) all: 0.091 / Net I/σ(I): 11.45 |
Reflection shell | Resolution: 3.0567→3.166 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 3885 / CC1/2: 0.63 / % possible all: 98.16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J8U Resolution: 3.057→36.287 Å / Cross valid method: FREE R-VALUE / σ(F): 102.78 / Phase error: 33.14 Details: The twin operator l,-k,h was used at the last stage of refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.057→36.287 Å
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Refine LS restraints |
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LS refinement shell |
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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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