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- PDB-3ayl: X-ray crystal structures of L-phenylalanine oxidase (deaminating ... -

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Basic information

Entry
Database: PDB / ID: 3ayl
TitleX-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism
ComponentsPro-enzyme of L-phenylalanine oxidase
KeywordsOXIDOREDUCTASE / L-PHENYLALANINE OXIDASE / AMINO ACID OXIDASE / FLAVOENZYME / L-Met Binding
Function / homology
Function and homology information


phenylalanine 2-monooxygenase / phenylalanine 2-monooxygenase activity / nucleotide binding
Similarity search - Function
Polyamine Oxidase; Chain A, domain 2 - #60 / Polyamine Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / METHIONINE / Phenylalanine 2-monooxygenase precursor
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSuzuki, H.
CitationJournal: J.Biochem. / Year: 2011
Title: High resolution X-ray crystal structures of L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism
Authors: Ida, K. / Suguro, M. / Suzuki, H.
History
DepositionMay 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Pro-enzyme of L-phenylalanine oxidase
B: Pro-enzyme of L-phenylalanine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,04510
Polymers155,7992
Non-polymers2,2468
Water40,0112221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-10 kcal/mol
Surface area42500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.269, 112.843, 136.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pro-enzyme of L-phenylalanine oxidase


Mass: 77899.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: P-501 / Gene: propao / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5W9R9, phenylalanine 2-monooxygenase

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Non-polymers , 5 types, 2229 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2221 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES PH 7.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→36.27 Å / Num. obs: 415723 / % possible obs: 97.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.347 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YR4

2yr4


Resolution: 1.25→36.27 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.77 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.128 20873 5 %RANDOM
Rwork0.099 ---
obs0.101 394789 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.25→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 146 2221 12791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02210844
X-RAY DIFFRACTIONr_bond_other_d0.0020.027116
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.96414818
X-RAY DIFFRACTIONr_angle_other_deg1.183.00117220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67751362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87623.262466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.868151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6591572
X-RAY DIFFRACTIONr_chiral_restr0.1470.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022260
X-RAY DIFFRACTIONr_nbd_refined0.2690.22462
X-RAY DIFFRACTIONr_nbd_other0.2280.28183
X-RAY DIFFRACTIONr_nbtor_refined0.1930.25424
X-RAY DIFFRACTIONr_nbtor_other0.0950.25398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1540.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.2113
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8171.58580
X-RAY DIFFRACTIONr_mcbond_other0.8971.52770
X-RAY DIFFRACTIONr_mcangle_it3.356210904
X-RAY DIFFRACTIONr_scbond_it4.9434787
X-RAY DIFFRACTIONr_scangle_it6.3384.53914
X-RAY DIFFRACTIONr_rigid_bond_restr2.37322274
X-RAY DIFFRACTIONr_sphericity_free20.58452221
X-RAY DIFFRACTIONr_sphericity_bonded6.962517686
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 1565 -
Rwork0.125 29322 -
obs--98.12 %

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