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- PDB-4q3w: Crystal structure of C. violaceum phenylalanine hydroxylase D139E... -

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Basic information

Entry
Database: PDB / ID: 4q3w
TitleCrystal structure of C. violaceum phenylalanine hydroxylase D139E mutation
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / Mutation / hydroxylase / phenylalanine hydroxylase / kinetics / metals / Chromobacterium / phenylketonurias / biopterin / Mixed alpha helix-beta sheet
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
: / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRonau, J.A. / Abu-Omar, M.M. / Das, C.
CitationJournal: Biochemistry / Year: 2014
Title: A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis.
Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Liedl, K.R. / Abu-Omar, M.M. / Das, C.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.2Sep 20, 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 / 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)33,7823
Polymers33,6611
Non-polymers1212
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.003, 38.673, 47.813
Angle α, β, γ (deg.)76.66, 72.86, 85.60
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33661.043 Da / Num. of mol.: 1 / Mutation: D139E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: phhA, CV_3180 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLySs / References: UniProt: P30967, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Na-HEPES, pH 7.0, 10 mM Magnesium chloride hexahydrate, 5 mM Nickel(II) chloride hexahydrate, 15% w/v polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 16, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 46304 / Num. obs: 44359 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.42 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LTU

1ltu


Resolution: 1.4→22.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.319 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19661 2347 5.1 %RANDOM
Rwork0.15782 ---
obs0.15977 43956 95.7 %-
all-45931 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 5 180 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192299
X-RAY DIFFRACTIONr_bond_other_d0.0010.022155
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9623133
X-RAY DIFFRACTIONr_angle_other_deg0.78634952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83223.604111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25115359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3121515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
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_restr1.37534454
X-RAY DIFFRACTIONr_sphericity_free28.489563
X-RAY DIFFRACTIONr_sphericity_bonded9.94254507
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 155 -
Rwork0.2 3121 -
obs--91.69 %

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