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- PDB-5den: The First Structure of a Full-Length Mammalian Phenylalanine Hydr... -

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Basic information

Entry
Database: PDB / ID: 5den
TitleThe First Structure of a Full-Length Mammalian Phenylalanine Hydroxylase Reveals the Architecture of an Auto-inhibited Tetramer
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / mammalian phenylalanine hydroxylase / allosteric regulation by phenylalanine / phenylketonuria / ACT-containing
Function / homology
Function and homology information


tyrosine biosynthetic process, by oxidation of phenylalanine / Phenylalanine metabolism / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / L-phenylalanine catabolic process / amino acid binding / iron ion binding / identical protein binding
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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsArturo, E.C. / Loll, P.J. / Jaffe, E.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer.
Authors: Arturo, E.C. / Gupta, K. / Heroux, A. / Stith, L. / Cross, P.J. / Parker, E.J. / Loll, P.J. / Jaffe, E.K.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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)207,7108
Polymers207,4864
Non-polymers2234
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-122 kcal/mol
Surface area68690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.780, 89.160, 196.810
Angle α, β, γ (deg.)90.000, 104.530, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 22 and (name N or name...
21(chain B and ((resid 22 and (name O or name...
31(chain C and ((resid 22 and (name N or name...
41(chain D and ((resid 22 and (name N or name...

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Components

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


Mass: 51871.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pah / Production host: Escherichia coli (E. coli) / References: UniProt: P04176, phenylalanine 4-monooxygenase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein was stored at -80C, then thawed in a water bath at 25C for ~ 20 minutes. The protein, at a concentration of 9.5 mg/mL was diluted to 5.5 mg/mL using 30 mM Tris pH 7.4, 116 mM KCl, ...Details: Protein was stored at -80C, then thawed in a water bath at 25C for ~ 20 minutes. The protein, at a concentration of 9.5 mg/mL was diluted to 5.5 mg/mL using 30 mM Tris pH 7.4, 116 mM KCl, 15% glycerol. The diluted protein was left at 4C for ~ hours, then at room temperature for ~ 20 minutes prior to preparation of the crystallization tray. The 2 uL hanging drop (containing 1:1 protein:reservoir) hung over a reservoir solution containing 140 mM Na-acetate, 70 mM Na-citrate, 100 mM Na-cacodylate (pH 6.5), and 31.5% PEG 1,000 (Hampton Research).
Temp details: Temperature is approximate. Temperature maintenance was passive; crystal trays were stored in an incubator that remained off.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→38.1 Å / Num. obs: 38661 / % possible obs: 91.01 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.06
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.56 / % possible all: 76.49

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.10pre_2120: ???refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PHZ
Resolution: 2.9→38.1 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3031 1930 5 %
Rwork0.2384 36698 -
obs0.2417 38628 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.95 Å2 / Biso mean: 81.3783 Å2 / Biso min: 29.55 Å2
Refinement stepCycle: final / Resolution: 2.9→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13706 0 4 8 13718
Biso mean--61.38 55.63 -
Num. residues----1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214062
X-RAY DIFFRACTIONf_angle_d0.38119013
X-RAY DIFFRACTIONf_chiral_restr0.0372046
X-RAY DIFFRACTIONf_plane_restr0.0032481
X-RAY DIFFRACTIONf_dihedral_angle_d8.5498439
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7818X-RAY DIFFRACTION5.976TORSIONAL
12B7818X-RAY DIFFRACTION5.976TORSIONAL
13C7818X-RAY DIFFRACTION5.976TORSIONAL
14D7818X-RAY DIFFRACTION5.976TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-2.97260.40581110.36142142225375
2.9726-3.05290.39111260.31222386251283
3.0529-3.14270.33021420.28392711285394
3.1427-3.24410.38461420.28582714285696
3.2441-3.360.35091440.28882732287696
3.36-3.49440.37751410.27652691283294
3.4944-3.65330.29811420.25762689283193
3.6533-3.84580.3361420.25412702284494
3.8458-4.08640.32061390.23272625276491
4.0864-4.40150.28271400.20932660280092
4.4015-4.84370.25631410.1892681282293
4.8437-5.54270.27871400.20362670281092
5.5427-6.97630.30151400.23772647278791
6.9763-38.10670.24831400.22492648278889
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8967-2.00881.00415.1156-1.36320.6034-0.1944-0.27570.0580.58760.33790.42950.2522-0.3415-0.10731.02290.00530.01740.53120.05390.3858-29.254830.190980.6921
20.841-0.23540.02630.8886-0.15911.52420.085-0.0383-0.29210.0197-0.02150.02590.3656-0.0218-0.05421.0062-0.064-0.10840.34350.04140.3645-6.22411.376171.2624
32.54731.0730.53123.5746-0.12071.447-0.18760.4381-0.1184-0.5437-0.0437-0.37820.2306-0.05590.2120.41290.04940.12770.4077-0.02980.27432.483328.177718.6672
41.45590.10060.2951.6752-0.18481.36210.09240.1329-0.49390.0572-0.03990.01660.2752-0.1444-0.040.75980.0821-0.05820.3095-0.06020.4367-21.179910.547427.6726
51.5839-1.38990.044.1815-0.24191.23050.28560.06640.3838-0.0459-0.2591-0.9117-0.75220.4153-0.06070.4623-0.04490.07820.38210.02940.254617.379631.735462.1777
60.7881-0.12230.01661.1742-0.24350.667-0.0127-0.07710.1998-0.2377-0.03580.0287-0.47880.04240.05461.1514-0.0572-0.06420.3690.0080.4095-5.367750.143570.8076
71.87290.8483-0.52616.5427-2.29912.0095-0.02330.2652-0.1378-0.56660.1291-0.05060.207-0.0587-0.13410.46990.0360.1060.3958-0.01130.3206-45.616832.177331.5803
81.8887-0.2010.25670.81420.17551.626-0.03830.29250.6440.2796-0.0004-0.1118-0.47620.06670.03010.72450.02120.04530.38070.04650.3182-21.796349.177323.7322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 22 through 115)A0
2X-RAY DIFFRACTION2chain A and (resid 116 through 450)A0
3X-RAY DIFFRACTION3chain B and (resid 22 through 115)B0
4X-RAY DIFFRACTION4chain B and (resid 116 through 447)B0
5X-RAY DIFFRACTION5chain C and (resid 21 through 115)C0
6X-RAY DIFFRACTION6chain C and (resid 116 through 447)C0
7X-RAY DIFFRACTION7chain D and (resid 20 through 115)D0
8X-RAY DIFFRACTION8chain D and (resid 116 through 449)D0

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