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- PDB-5fgj: Structure of tetrameric rat phenylalanine hydroxylase, residues 1-453 -

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Basic information

Entry
Database: PDB / ID: 5fgj
TitleStructure of tetrameric rat phenylalanine hydroxylase, residues 1-453
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / phenylketonuria / PKU mutation / allostery / ACT domain
Function / homology
Function and homology information


L-tyrosine biosynthetic process, by oxidation of phenylalanine / Phenylalanine metabolism / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-tyrosine biosynthetic process / L-phenylalanine catabolic process / amino acid binding / iron ion binding / identical protein binding
Similarity search - Function
Phenylalanine-4-hydroxylase, tetrameric form / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / ACT domain / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal ...Phenylalanine-4-hydroxylase, tetrameric form / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / ACT domain / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / ACT domain profile. / ACT domain / ACT-like domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsTaylor, A.B. / Roberts, K.M. / Fitzpatrick, P.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering.
Authors: Meisburger, S.P. / Taylor, A.B. / Khan, C.A. / Zhang, S. / Fitzpatrick, P.F. / Ando, N.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
B: Phenylalanine-4-hydroxylase
C: Phenylalanine-4-hydroxylase
D: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,7909
Polymers207,5424
Non-polymers2485
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-117 kcal/mol
Surface area67990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.768, 102.686, 202.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phenylalanine-4-hydroxylase / PAH / Phe-4-monooxygenase


Mass: 51885.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pah / Plasmid: pERPH / Production host: Escherichia coli (E. coli) / References: UniProt: P04176, phenylalanine 4-monooxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M bis-tris:HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.6→102.69 Å / Num. obs: 24188 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 75.6 Å2 / Rsym value: 0.388 / Net I/σ(I): 6.5
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.287 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1688 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PHM

2phm


Resolution: 3.6→101.48 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2008 8.32 %Random selection
Rwork0.2679 ---
obs0.2702 24126 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→101.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13807 0 5 0 13812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214141
X-RAY DIFFRACTIONf_angle_d0.56319146
X-RAY DIFFRACTIONf_dihedral_angle_d11.9375277
X-RAY DIFFRACTIONf_chiral_restr0.0612064
X-RAY DIFFRACTIONf_plane_restr0.0042498
LS refinement shellResolution: 3.6→3.69 Å
RfactorNum. reflection% reflection
Rfree0.3573 143 -
Rwork0.3601 1568 -
obs--100 %

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