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- PDB-2yr6: Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501 -

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Basic information

Entry
Database: PDB / ID: 2yr6
TitleCrystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501
ComponentsPro-enzyme of L-phenylalanine oxidase
KeywordsOXIDOREDUCTASE / L-phenylalanine oxidase / amino oxidase / flavoenzyme
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
2-AMINOBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Phenylalanine 2-monooxygenase precursor
Similarity search - Component
Biological speciesPseudomonas sp. P-501 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsIda, K. / Kurabayashi, M. / Suguro, M. / Suzuki, H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis of proteolytic activation of L-phenylalanine oxidase from Pseudomonas sp. P-501.
Authors: Ida, K. / Kurabayashi, M. / Suguro, M. / Hiruma, Y. / Hikima, T. / Yamomoto, M. / Suzuki, H.
History
DepositionApr 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Oct 25, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)158,02110
Polymers155,7992
Non-polymers2,2228
Water35,2551957
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-35.6 kcal/mol
Surface area41360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.877, 113.029, 136.463
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 sp. P-501 (bacteria) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5W9R9, phenylalanine 2-monooxygenase

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Non-polymers , 5 types, 1965 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-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#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.: 1957 / 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: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH7.5, 1.0M ammonium sulfate, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→34.18 Å / Num. obs: 339311 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.342 / % possible all: 100

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Processing

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

2yr4


Resolution: 1.35→34.18 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.122 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13769 17132 5.1 %RANDOM
Rwork0.10263 ---
obs0.10439 322071 99.82 %-
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: 12.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 148 1957 12529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.02210848
X-RAY DIFFRACTIONr_bond_other_d0.0020.027116
X-RAY DIFFRACTIONr_angle_refined_deg2.4751.96614826
X-RAY DIFFRACTIONr_angle_other_deg1.273.00117212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74451362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6223.262466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.858151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2951572
X-RAY DIFFRACTIONr_chiral_restr0.1740.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022274
X-RAY DIFFRACTIONr_nbd_refined0.2510.22377
X-RAY DIFFRACTIONr_nbd_other0.2250.27964
X-RAY DIFFRACTIONr_nbtor_refined0.1930.25430
X-RAY DIFFRACTIONr_nbtor_other0.0970.25478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.21333
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.275
X-RAY DIFFRACTIONr_mcbond_it3.3391.58518
X-RAY DIFFRACTIONr_mcbond_other1.1531.52776
X-RAY DIFFRACTIONr_mcangle_it3.911210894
X-RAY DIFFRACTIONr_scbond_it5.76534786
X-RAY DIFFRACTIONr_scangle_it7.154.53932
X-RAY DIFFRACTIONr_rigid_bond_restr2.928322278
X-RAY DIFFRACTIONr_sphericity_free24.11951957
X-RAY DIFFRACTIONr_sphericity_bonded8.167517688
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 1220 -
Rwork0.129 23748 -
obs--100 %

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