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- PDB-2phm: STRUCTURE OF PHENYLALANINE HYDROXYLASE DEPHOSPHORYLATED -

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Basic information

Entry
Database: PDB / ID: 2phm
TitleSTRUCTURE OF PHENYLALANINE HYDROXYLASE DEPHOSPHORYLATED
ComponentsPROTEIN (PHENYLALANINE-4-HYDROXYLASE)
KeywordsOXIDOREDUCTASE / PHENYLALANINE HYDROXYLASE / AROMATIC AMINO ACID HYDROXYLASE / PHOSPHORYLATION / INTRASTERIC REGULATION / ALLOSTERIC REGULATION
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 / MIRAS / Resolution: 2.6 Å
AuthorsKobe, B. / Jennings, I.G. / House, C.M. / Michell, B.J. / Cotton, R.G. / Kemp, B.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural basis of autoregulation of phenylalanine hydroxylase.
Authors: Kobe, B. / Jennings, I.G. / House, C.M. / Michell, B.J. / Goodwill, K.E. / Santarsiero, B.D. / Stevens, R.C. / Cotton, R.G. / Kemp, B.E.
#1: Journal: Protein Sci. / Year: 1997
Title: Regulation and Crystallization of Phosphorylated and Dephosphorylated Forms of Truncated Dimeric Phenylalanine Hydroxylase
Authors: Kobe, B. / Jennings, I.G. / House, C.M. / Feil, S.C. / Michell, B.J. / Tiganis, T. / Parker, M.W. / Cotton, R.G.H. / Kemp, B.E.
History
DepositionNov 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 30, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHENYLALANINE-4-HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3852
Polymers49,3301
Non-polymers561
Water2,018112
1
A: PROTEIN (PHENYLALANINE-4-HYDROXYLASE)
hetero molecules

A: PROTEIN (PHENYLALANINE-4-HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7714
Polymers98,6592
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Unit cell
Length a, b, c (Å)56.433, 56.433, 299.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PROTEIN (PHENYLALANINE-4-HYDROXYLASE) / PHENYLALANINE 4-MONOOXYGENASE


Mass: 49329.543 Da / Num. of mol.: 1 / Fragment: PHEOH-24 (RESIDUES 1-429)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04176, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.42 Å3/Da / Density % sol: 48.7 %
Crystal growpH: 8
Details: 23-25% PEG 4000 100 MM TRIS-HCL PH 8.0 0-5 MM GLUTATHIONE
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.85 mg/mlprotein1drop
220 %PEG40001reservoir
3100 mMsodium citrate1reservoir
40.25 %t-butanol1reservoir
510 mMfree glutathione1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. obs: 15307 / % possible obs: 95 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / % possible all: 95
Reflection
*PLUS
Num. measured all: 105530
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHARPphasing
SOLOMONphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS
Starting model: 1-H

Resolution: 2.6→99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 997 6.5 %RANDOM
Rwork0.208 ---
obs-15312 95.9 %-
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-99 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 1 112 3398
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.951.5
X-RAY DIFFRACTIONx_mcangle_it4.52
X-RAY DIFFRACTIONx_scbond_it4.32
X-RAY DIFFRACTIONx_scangle_it5.782.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 114 7.7 %
Rwork0.29 1371 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2FE.PARWATFE.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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