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- PDB-6hpo: Crystallographic structure of the catalytic domain of Human Pheny... -

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Basic information

Entry
Database: PDB / ID: 6hpo
TitleCrystallographic structure of the catalytic domain of Human Phenylalanine Hydroxylase (hPAH CD) in complex with iron at 1.6 Angstrom
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / Tetrahydrobiopterin / amino acid hydroxylases / phenylketonuria / allosteric regulation / METAL BINDING PROTEIN
Function / homology
Function and homology information


phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / catecholamine biosynthetic process / L-phenylalanine catabolic process / neurotransmitter biosynthetic process / cellular amino acid biosynthetic process / iron ion binding / cytosol
Aromatic amino acid hydroxylase, iron/copper binding site / Phenylalanine-4-hydroxylase, tetrameric form / ACT domain / Biopterin-dependent aromatic amino acid hydroxylase / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Aromatic amino acid hydroxylase superfamily / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase, C-terminal / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase ...Aromatic amino acid hydroxylase, iron/copper binding site / Phenylalanine-4-hydroxylase, tetrameric form / ACT domain / Biopterin-dependent aromatic amino acid hydroxylase / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Aromatic amino acid hydroxylase superfamily / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase, C-terminal / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase / ACT domain / Aromatic amino acid hydroxylase / Phenylalanine Hydroxylase / Orthogonal Bundle / Mainly Alpha
Phenylalanine-4-hydroxylase
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsAlcorlo Pages, M. / Innselset Flydal, M.
Funding support Spain, Norway, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-59389-P and BFU2017-90030-P to JAH Spain
Research Council of NorwayPrograms Forny (248889/O30) and FRIMEDBIO (261826) to AM Norway
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9852
Polymers51,9291
Non-polymers561
Water5,296294
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)65.856, 107.549, 124.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 51928.906 Da / Num. of mol.: 1
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-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.: 294 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 40 mM PIPES, 20% PEG 2000, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.67→32.77 Å / Num. obs: 51389 / % possible obs: 99.96 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 1.921 / Num. unique obs: 2603 / Rpim(I) all: 0.574

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ANP
Resolution: 1.67→32.77 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.41
RfactorNum. reflection% reflection
Rfree0.177 2541 4.95 %
Rwork0.1607 --
Obs0.1615 51335 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 1 294 2835
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062680
X-RAY DIFFRACTIONf_angle_d0.7733651
X-RAY DIFFRACTIONf_dihedral_angle_d5.8822208
X-RAY DIFFRACTIONf_chiral_restr0.05382
X-RAY DIFFRACTIONf_plane_restr0.005476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.67-1.70210.30071450.27322706X-RAY DIFFRACTION100
1.7021-1.73690.28131310.25322671X-RAY DIFFRACTION100
1.7369-1.77460.23471360.2252656X-RAY DIFFRACTION100
1.7746-1.81590.22341320.21072696X-RAY DIFFRACTION100
1.8159-1.86130.21071130.19992718X-RAY DIFFRACTION100
1.8613-1.91160.20941460.18822681X-RAY DIFFRACTION100
1.9116-1.96790.20441270.1672706X-RAY DIFFRACTION100
1.9679-2.03140.1791400.15962681X-RAY DIFFRACTION100
2.0314-2.1040.17261610.15852687X-RAY DIFFRACTION100
2.104-2.18820.18221520.16262660X-RAY DIFFRACTION100
2.1882-2.28780.19891410.15832709X-RAY DIFFRACTION100
2.2878-2.40840.18331490.15962680X-RAY DIFFRACTION100
2.4084-2.55920.17731440.15642721X-RAY DIFFRACTION100
2.5592-2.75670.20381450.16512726X-RAY DIFFRACTION100
2.7567-3.0340.18211530.1632708X-RAY DIFFRACTION100
3.034-3.47260.17671330.15682754X-RAY DIFFRACTION100
3.4726-4.37340.16011590.13662739X-RAY DIFFRACTION100
4.3734-32.93440.14021340.15452895X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.1353 Å / Origin y: 24.8754 Å / Origin z: 9.606 Å
111213212223313233
T0.2107 Å20.0059 Å20.0035 Å2-0.2229 Å2-0.0025 Å2--0.2037 Å2
L1.071 °2-0.209 °2-0.1755 °2-0.7995 °20.1815 °2--0.6804 °2
S-0.0217 Å °-0.0939 Å °-0.0357 Å °-0.0221 Å °0.0171 Å °-0.0176 Å °-0.0102 Å °-0.0493 Å °0.0063 Å °
Refinement TLS groupSelection details: all

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