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- PDB-1lrm: Crystal structure of binary complex of the catalytic domain of hu... -

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Basic information

Entry
Database: PDB / ID: 1lrm
TitleCrystal structure of binary complex of the catalytic domain of human phenylalanine hydroxylase with dihydrobiopterin (BH2)
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / BASKET-ARRANGEMENT / 13 ALPHA-HELICES / 6 BETA-STRANDS / FERRIC IRON
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
: / 7,8-DIHYDROBIOPTERIN / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Starting with 1PAH phases / Resolution: 2.1 Å
AuthorsAndersen, O.A.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8973
Polymers37,6021
Non-polymers2952
Water3,495194
1
A: Phenylalanine-4-hydroxylase
hetero molecules

A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7936
Polymers75,2032
Non-polymers5904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)66.588, 108.117, 124.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological dimer is generated by: -x, y, -z+1/2.

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Components

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


Mass: 37601.570 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (RESIDUES 103-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Plasmid: PMAL / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 2000, 11% ethylene glycol 0.12M Na-Hepes pH 6.8, 5mM BH2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 26185 / Num. obs: 26185 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 23 / Num. unique all: 3829 / Rsym value: 0.318 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Starting with 1PAH phases
Starting model: PDB ENTRY 1PAH

1pah


Resolution: 2.1→10 Å / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2579 -RANDOM
Rwork0.211 ---
all-26185 --
obs-26185 100 %-
Displacement parametersBiso mean: 27.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-10 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 18 194 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shellResolution: 2.1→2.11 Å /
RfactorNum. reflection
Rfree0.323 50
Rwork0.272 -
obs-537

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