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- PDB-6n1k: Full-length human phenylalanine hydroxylase (PAH) in the resting state -

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Basic information

Entry
Database: PDB / ID: 6n1k
TitleFull-length human phenylalanine hydroxylase (PAH) in the resting state
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / resting-state PAH / allosterically controlled aromatic amino acid hydroxylase
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: 3.057 Å
AuthorsArturo, E.C. / Jaffe, E.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS100081-03 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium.
Authors: Arturo, E.C. / Gupta, K. / Hansen, M.R. / Borne, E. / Jaffe, E.K.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)207,49212
Polymers207,1274
Non-polymers3658
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-147 kcal/mol
Surface area70960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.437, 202.640, 72.574
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Phenylalanine-4-hydroxylase / PAH / Phe-4-monooxygenase


Mass: 51781.648 Da / Num. of mol.: 4 / Mutation: C29S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hPAH C29S was obtained from of the 6His-SUMO fusion using a sodium phosphate buffer. Crystals were grown from C29S (16 mg/mL) in 2 mM Tris-HCl pH 7.4, mixed with reservoir solutions in a ...Details: hPAH C29S was obtained from of the 6His-SUMO fusion using a sodium phosphate buffer. Crystals were grown from C29S (16 mg/mL) in 2 mM Tris-HCl pH 7.4, mixed with reservoir solutions in a protein:reservoir ratio equal to 1:1.25 and equilibrated using hanging drop vapor diffusion. The 1 mL reservoir solution initially contained 16% PEG 3350, 100 mM bis-tris-propane pH 7.5 and 200 mM sodium sulfate. Crystals appeared at 295K within one day in the dark.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.008 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.05→37 Å / Num. obs: 39316 / % possible obs: 99.54 % / Redundancy: 3.9 % / Biso Wilson estimate: 93.6345104659 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0783 / Rrim(I) all: 0.091 / Net I/σ(I): 11.45
Reflection shellResolution: 3.0567→3.166 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 3885 / CC1/2: 0.63 / % possible all: 98.16

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.12rc1_2807phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8U

1j8u


Resolution: 3.057→36.287 Å / Cross valid method: FREE R-VALUE / σ(F): 102.78 / Phase error: 33.14
Details: The twin operator l,-k,h was used at the last stage of refinement.
RfactorNum. reflection% reflection
Rfree0.238 1985 5.05 %
Rwork0.2025 --
obs0.2076 39316 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.057→36.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13674 0 8 7 13689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214031
X-RAY DIFFRACTIONf_angle_d0.518954
X-RAY DIFFRACTIONf_dihedral_angle_d9.6718418
X-RAY DIFFRACTIONf_chiral_restr0.0382049
X-RAY DIFFRACTIONf_plane_restr0.0032449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.058-3.13450.32971450.29562608X-RAY DIFFRACTION93
3.1345-3.21920.30241470.28462670X-RAY DIFFRACTION95
3.2192-3.31380.29491420.27832701X-RAY DIFFRACTION95
3.3138-3.42070.28511460.26862634X-RAY DIFFRACTION95
3.4207-3.54280.28031440.2552652X-RAY DIFFRACTION95
3.5428-3.68450.28151320.22842668X-RAY DIFFRACTION95
3.6845-3.8520.23611400.21782669X-RAY DIFFRACTION95
3.852-4.05470.2671410.21232676X-RAY DIFFRACTION95
4.0547-4.30830.21041390.1982668X-RAY DIFFRACTION95
4.3083-4.64020.20621450.17832651X-RAY DIFFRACTION95
4.6402-5.10580.20581400.16982672X-RAY DIFFRACTION95
5.1058-5.84150.24021350.19642652X-RAY DIFFRACTION95
5.8415-7.34760.22891460.19362710X-RAY DIFFRACTION95
7.3476-34.16390.22461380.18582688X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26950.4448-0.28551.25420.07293.014-0.2063-0.07350.0796-0.0918-0.07470.10570.1092-0.5428-00.93990.02620.10820.6440.00850.723940.072199.950655.8022
21.56260.0072-0.98111.80240.04032.2966-0.1068-0.05890.0454-0.0145-0.0479-0.31390.12110.389-00.96230.13820.19830.63050.01470.892469.9877103.389941.1735
32.9633-0.3571-0.1431.35780.00492.68690.219-0.44490.11350.00120.0165-0.14690.05930.096800.8354-0.05370.13880.6238-0.12530.907952.38854.515169.6081
41.6453-0.201-0.93662.1566-0.00652.13610.22450.2740.1257-0.3043-0.0165-0.0615-0.1195-0.075200.9729-0.110.23910.66260.01430.928467.127452.246639.6581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resid 21 through 446
2X-RAY DIFFRACTION2chain 'B' and resid 20 through 448
3X-RAY DIFFRACTION3chain 'C' and resid 22 through 448
4X-RAY DIFFRACTION4chain 'D' and resid 20 through 446

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