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- PDB-1mmt: Crystal structure of ternary complex of the catalytic domain of h... -

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Basic information

Entry
Database: PDB / ID: 1mmt
TitleCrystal structure of ternary complex of the catalytic domain of human phenylalanine hydroxylase (Fe(II)) complexed with tetrahydrobiopterin and norleucine
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / BASKET-ARRANGEMENT / 13 ALPHA-HELICES / 8 BETA-STRANDS / FERROUS IRON
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 / NORLEUCINE / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / phases adopted from 1KW0 / Resolution: 2 Å
AuthorsAndersen, O.A. / Flatmark, T. / Hough, E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate ...Title: 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate specificity and molecular motions related to substrate binding
Authors: Andersen, O.A. / Stokka, A.J. / Flatmark, T. / Hough, E.
History
DepositionSep 4, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)38,1265
Polymers37,6021
Non-polymers5244
Water2,684149
1
A: Phenylalanine-4-hydroxylase
hetero molecules

A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25210
Polymers75,2032
Non-polymers1,0498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)65.140, 106.638, 123.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE SECOND PART OF THE BIOLOGICAL DIMER IS GENERATED BY: -x, y, 1/2-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenylalanine-4-hydroxylase


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

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Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3
#5: Chemical ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 2000, 12% ethylene glycol, 0.12M Na-Hepes, 10mM BH4, 30mM Na-dithionite, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG20001reservoir
212 %(v/v)ethylene glycol1reservoir
30.12 Msodium HEPES1reservoirpH6.8
410 mM1reservoirBH4
530 mMsodium dithionite1reservoir
67-8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28552 / Num. obs: 28552 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4197 / Rsym value: 0.275 / % possible all: 99.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 4197

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: phases adopted from 1KW0
Starting model: PDB ENTRY 1KW0

1kw0


Resolution: 2→10 Å / Isotropic thermal model: overall anisotropic b value / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2803 -random
Rwork0.213 ---
all-25498 --
obs-25498 89.3 %-
Displacement parametersBiso mean: 28.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 32 149 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.01 Å /
RfactorNum. reflection
Rfree0.266 55
Rwork0.277 -
obs-590
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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