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- PDB-1j8u: Catalytic Domain of Human Phenylalanine Hydroxylase Fe(II) in Com... -

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Basic information

Entry
Database: PDB / ID: 1j8u
TitleCatalytic Domain of Human Phenylalanine Hydroxylase Fe(II) in Complex with Tetrahydrobiopterin
ComponentsPHENYLALANINE-4-HYDROXYLASE
KeywordsOXIDOREDUCTASE / ferrous iron / 2-His-1-carboxylate facial triad / tetrahydrobiopterin
Function / homology
Function and homology information


Phenylketonuria / phenylalanine 4-monooxygenase / Phenylalanine metabolism / phenylalanine 4-monooxygenase activity / L-tyrosine biosynthetic process / catecholamine biosynthetic process / L-phenylalanine catabolic process / amino acid biosynthetic process / iron ion binding / cytosol
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
: / 5,6,7,8-TETRAHYDROBIOPTERIN / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsAndersen, O.A. / Flatmark, T. / Hough, E.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: High resolution crystal structures of the catalytic domain of human phenylalanine hydroxylase in its catalytically active Fe(II) form and binary complex with tetrahydrobiopterin.
Authors: Andersen, O.A. / Flatmark, T. / Hough, E.
History
DepositionMay 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE-4-HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8993
Polymers37,6021
Non-polymers2972
Water7,080393
1
A: PHENYLALANINE-4-HYDROXYLASE
hetero molecules

A: PHENYLALANINE-4-HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7976
Polymers75,2032
Non-polymers5944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)66.441, 108.676, 124.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PHENYLALANINE-4-HYDROXYLASE / PHE-4-MONOOXYGENASE


Mass: 37601.570 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (Residues 103-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.98 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop, anaerobically / pH: 6.8
Details: PEG2000, Na-hepes, ethylene glycol, pH 6.8, Vapor diffusion, hanging drop, anaerobically, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1reservoirBH4
2150 mMdithiothreitol1reservoir
35.5 mg/mlprotein1drop
420 mMsodium-Hepes1droppH6.8
575 mM1dropNaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 71940 / Num. obs: 71940 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / Num. unique all: 10450 / Rsym value: 0.37 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 495560 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 100 % / Num. possible: 10450 / Num. measured obs: 61233 / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: PDB entry 1PAH

1pah


Resolution: 1.5→10 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber, 1991
RfactorNum. reflection% reflectionSelection details
Rfree0.203 7274 -Random
Rwork0.155 ---
all0.157 71887 --
obs0.157 71887 100 %-
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 18 393 2943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d2.03
X-RAY DIFFRACTIONs_dihedral_angle_d23.8
X-RAY DIFFRACTIONs_improper_angle_d1.26
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.157 / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.03
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg23.8
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.26

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