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- PDB-1tg2: Crystal structure of phenylalanine hydroxylase A313T mutant with ... -

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Basic information

Entry
Database: PDB / ID: 1tg2
TitleCrystal structure of phenylalanine hydroxylase A313T mutant with 7,8-dihydrobiopterin bound
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / phenylalanine hydroxylase phenylketonuria mutant A313T in complex with cofactor analogue 7 / 8-dihydrobiopterin
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
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
: / Chem-H2B / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Difference fourier / Resolution: 2.2 Å
AuthorsErlandsen, H. / Pey, A.L. / Gamez, A. / Perez, B. / Desviat, L.R. / Aguado, C. / Koch, R. / Surendran, S. / Tyring, S. / Matalon, R. ...Erlandsen, H. / Pey, A.L. / Gamez, A. / Perez, B. / Desviat, L.R. / Aguado, C. / Koch, R. / Surendran, S. / Tyring, S. / Matalon, R. / Scriver, C.R. / Ugarte, M. / Martinez, A. / Stevens, R.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Correction of kinetic and stability defects by tetrahydrobiopterin in phenylketonuria patients with certain phenylalanine hydroxylase mutations.
Authors: Erlandsen, H. / Pey, A.L. / Gamez, A. / Perez, B. / Desviat, L.R. / Aguado, C. / Koch, R. / Surendran, S. / Tyring, S. / Matalon, R. / Scriver, C.R. / Ugarte, M. / Martinez, A. / Stevens, R.C.
History
DepositionMay 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,0263
Polymers35,7311
Non-polymers2952
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.534, 107.755, 124.282
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 / PAH / Phe-4- monooxygenase


Mass: 35730.543 Da / Num. of mol.: 1
Fragment: Delta NH 1-102-Delta COOH 428 human phenylalanine hydroxylase
Mutation: A313T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Plasmid: pMALc2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-H2B / 2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE / QUINONOID 7,8-TETRAHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.196 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 5-10% Ethylene Glycol, 20-40 mM Pipes, pH 6.8, 8-15% PEG 2000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 13, 2003 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 22757 / Num. obs: 22757 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.194 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 20 / Num. unique all: 2260 / Rsym value: 0.815 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: Difference fourier
Starting model: 1LRM

1lrm


Resolution: 2.2→19.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 295349.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1075 4.9 %RANDOM
Rwork0.213 ---
all0.213 25644 --
obs0.213 22008 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0845 Å2 / ksol: 0.305909 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--3.51 Å20 Å2
3----4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 18 73 2617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it3.711.5
X-RAY DIFFRACTIONc_mcangle_it5.672
X-RAY DIFFRACTIONc_scbond_it7.462
X-RAY DIFFRACTIONc_scangle_it11.192.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 162 4.7 %
Rwork0.277 3281 -
obs-2260 90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3NEWFE.PARAMNEWFE.TOP
X-RAY DIFFRACTION4H2B.PARH2B.TOP

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