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- PDB-2pah: TETRAMERIC HUMAN PHENYLALANINE HYDROXYLASE -

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Basic information

Entry
Database: PDB / ID: 2pah
TitleTETRAMERIC HUMAN PHENYLALANINE HYDROXYLASE
ComponentsPROTEIN (PHENYLALANINE HYDROXYLASE)
KeywordsHYDROXYLASE / PHENYLKETONURIA
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
: / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsStevens, R.C. / Fusetti, F. / Erlandsen, H.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure of tetrameric human phenylalanine hydroxylase and its implications for phenylketonuria.
Authors: Fusetti, F. / Erlandsen, H. / Flatmark, T. / Stevens, R.C.
History
DepositionMay 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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: PROTEIN (PHENYLALANINE HYDROXYLASE)
B: PROTEIN (PHENYLALANINE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3964
Polymers77,2842
Non-polymers1122
Water00
1
A: PROTEIN (PHENYLALANINE HYDROXYLASE)
B: PROTEIN (PHENYLALANINE HYDROXYLASE)
hetero molecules

A: PROTEIN (PHENYLALANINE HYDROXYLASE)
B: PROTEIN (PHENYLALANINE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,7918
Polymers154,5684
Non-polymers2234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+2/31
Buried area10460 Å2
ΔGint-109 kcal/mol
Surface area55710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.500, 119.500, 126.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein PROTEIN (PHENYLALANINE HYDROXYLASE) / PAH


Mass: 38641.926 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-452
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE IRON ATOM FE / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-3A-D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe

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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: 3.36 Å3/Da / Density % sol: 60 %
Crystal growpH: 7
Details: 0.6 M MGSO4, 0.2 M NAK TARTRATE, 10% PEG-4000, 0.1 M BIS-TRIS PROPANE (PH 7.0)
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 M1reservoirMe2SO
20.2 Msodium potassium tartrate1reservoir
310 %PEG40001reservoir
4100 mMBis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 120922 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2 / Rsym value: 0.25 / % possible all: 98
Reflection
*PLUS
Num. obs: 18446 / Num. measured all: 120922

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TOH

1toh


Resolution: 3.1→20 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1800 10 %RANDOM
Rwork0.251 ---
obs0.251 18446 99.9 %-
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5315 0 2 0 5317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.1→3.2 Å / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.326 10 %
Rwork0.251 -
obs-98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.7
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / Rfactor Rfree: 0.326 / % reflection Rfree: 10 % / Rfactor Rwork: 0.251

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