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Basic information

Entry
Database: PDB / ID: 4bpt
TitleStructural and thermodynamic insight into phenylalanine hydroxylase from the human pathogen Legionella pneumophila
ComponentsPHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
KeywordsOXIDOREDUCTASE / PYOMELANIN SYNTHESIS / THERMOSTABILITY / AGGREGATION
Function / homology
Function and homology information


phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-phenylalanine catabolic process / iron ion binding
Similarity search - Function
Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / 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 ...Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLeiros, H.-K.S. / Flydal, M.I. / Martinez, A.
CitationJournal: FEBS Open Bio / Year: 2013
Title: Structural and Thermodynamic Insight Into Phenylalanine Hydroxylase from the Human Pathogen Legionella Pneumophila.
Authors: Leiros, H.S. / Flydal, M.I. / Martinez, A.
History
DepositionMay 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Atomic model
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
B: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
C: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
D: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,31210
Polymers125,6754
Non-polymers6376
Water2,792155
1
A: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7374
Polymers31,4191
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7374
Polymers31,4191
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)


Theoretical massNumber of molelcules
Total (without water)31,4191
Polymers31,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)


Theoretical massNumber of molelcules
Total (without water)31,4191
Polymers31,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.320, 60.120, 124.040
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PHENYLALANINE-4-HYDROXYLASE (PAH) (PHE-4-MONOOXYGENASE)


Mass: 31418.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIL
References: UniProt: I7HM43, UniProt: Q5ZS72*PLUS, phenylalanine 4-monooxygenase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.67 Å3/Da / Density % sol: 53.98 % / Description: NONE
Crystal growDetails: 1.6 M NAK2PO4, 4% (V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 41892 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 0
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V27

2v27


Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.643 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.30203 1272 3.1 %RANDOM
Rwork0.2636 ---
obs0.26481 40034 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.801 Å2
Baniso -1Baniso -2Baniso -3
1--18.15 Å20 Å2-4.74 Å2
2---17.52 Å20 Å2
3---35.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7949 0 42 155 8146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.027868
X-RAY DIFFRACTIONr_bond_other_d0.0080.025439
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.96610682
X-RAY DIFFRACTIONr_angle_other_deg1.614313035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6755961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69423.352364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.129151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391547
X-RAY DIFFRACTIONr_chiral_restr0.1230.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218813
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 82 -
Rwork0.298 2804 -
obs--91.71 %
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)
11.09020.2554-0.11460.071-0.15441.4964-0.04050.0160.0302-0.0119-0.00310.00450.01650.10960.04360.03290.0001-0.0050.02130.02440.188717.567-0.734-4.551
20.2662-0.0129-0.10490.3710.12760.584-0.0343-0.03710.0316-0.02410.0304-0.00570.0460.04380.0040.01240.00170.00740.01260.00710.26245.433-0.0535.064
30.8080.15350.69870.04380.05321.1176-0.0136-0.02690.0259-0.00720.0216-0.0055-0.0362-0.1432-0.0080.04890.00290.05050.0539-0.03330.166927.636-20.148-4.458
40.268-0.18030.15620.3558-0.06120.5669-0.0228-0.0465-0.0283-0.01530.05320.0262-0.0242-0.0166-0.03050.00730.00060.02170.01030.00010.304939.707-20.8675.049
57.3743-2.1153.37661.26781.06517.8002-0.119-0.46440.08280.0260.2315-0.0766-0.09490.0709-0.11250.1970.0241-0.04440.1509-0.11070.097851.526-12.32646.652
60.5796-0.1723-1.13380.13250.56768.78560.8906-0.75720.3929-0.27130.3423-0.1554-1.11411.1864-1.23291.4441-1.24220.57211.231-0.54250.366152.302-12.24547.028
71.05153.03580.14838.85270.48920.0697-0.2066-0.02430.2481-0.42720.09530.81120.13350.08950.11140.630.23110.18180.34720.15010.1669-6.449-8.65246.673
80.7523.161-0.303613.5792-1.30410.1413-0.20520.02330.1542-1.04140.23420.6810.125-0.0046-0.02890.31730.110.08060.36310.19740.1921-6.927-8.42447.323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 49
2X-RAY DIFFRACTION2A50 - 261
3X-RAY DIFFRACTION3B10 - 49
4X-RAY DIFFRACTION4B50 - 261
5X-RAY DIFFRACTION5C30 - 49
6X-RAY DIFFRACTION6C50 - 261
7X-RAY DIFFRACTION7D30 - 49
8X-RAY DIFFRACTION8D50 - 261

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