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- PDB-5egq: Structure of tetrameric rat phenylalanine hydroxylase mutant R270... -

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Basic information

Entry
Database: PDB / ID: 5egq
TitleStructure of tetrameric rat phenylalanine hydroxylase mutant R270K, residues 25-453
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / hydroxylase / 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: 2.5 Å
AuthorsTaylor, A.B. / Khan, C.A. / 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
DepositionOct 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)208,00710
Polymers207,4304
Non-polymers5766
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15720 Å2
ΔGint-167 kcal/mol
Surface area65000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.144, 96.507, 202.584
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: 51857.566 Da / Num. of mol.: 4 / Mutation: R270K
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-tris:HCl, 25% PEG 3350, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→47.16 Å / Num. obs: 61203 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.096 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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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: 2.5→47.155 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1998 3.27 %Random selection
Rwork0.2112 ---
obs0.2126 61113 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13332 0 30 176 13538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713687
X-RAY DIFFRACTIONf_angle_d1.16418534
X-RAY DIFFRACTIONf_dihedral_angle_d12.8095094
X-RAY DIFFRACTIONf_chiral_restr0.0921998
X-RAY DIFFRACTIONf_plane_restr0.0082402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.37751520.29744180X-RAY DIFFRACTION99
2.5625-2.63180.34061430.28824202X-RAY DIFFRACTION100
2.6318-2.70920.32481410.26694176X-RAY DIFFRACTION99
2.7092-2.79670.29831360.26484227X-RAY DIFFRACTION100
2.7967-2.89660.3181410.25464201X-RAY DIFFRACTION99
2.8966-3.01260.31111560.24944212X-RAY DIFFRACTION99
3.0126-3.14970.28311340.24384181X-RAY DIFFRACTION99
3.1497-3.31570.30691390.23814152X-RAY DIFFRACTION97
3.3157-3.52340.28311390.22514219X-RAY DIFFRACTION99
3.5234-3.79530.2251460.19954248X-RAY DIFFRACTION99
3.7953-4.1770.23671430.17824255X-RAY DIFFRACTION99
4.177-4.78090.20341390.16314170X-RAY DIFFRACTION97
4.7809-6.02150.21751490.1894329X-RAY DIFFRACTION99
6.0215-47.1630.2051400.18064363X-RAY DIFFRACTION96

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