3AYL

X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YR4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52970.1M HEPES PH 7.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.550.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.269α = 90
b = 112.843β = 90
c = 136.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12APhoton FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2536.2797.40.0775415723
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3298.40.3474.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2YR41.2536.2739478920873970.1010.0990.128RANDOM10.52
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.51-0.11-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.876
r_dihedral_angle_4_deg21.659
r_sphericity_free20.584
r_dihedral_angle_3_deg11.868
r_sphericity_bonded6.962
r_dihedral_angle_1_deg6.677
r_scangle_it6.338
r_scbond_it4.94
r_mcangle_it3.356
r_mcbond_it2.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.876
r_dihedral_angle_4_deg21.659
r_sphericity_free20.584
r_dihedral_angle_3_deg11.868
r_sphericity_bonded6.962
r_dihedral_angle_1_deg6.677
r_scangle_it6.338
r_scbond_it4.94
r_mcangle_it3.356
r_mcbond_it2.817
r_rigid_bond_restr2.37
r_angle_refined_deg2.298
r_angle_other_deg1.18
r_mcbond_other0.897
r_symmetry_hbond_refined0.31
r_nbd_refined0.269
r_xyhbond_nbd_refined0.238
r_symmetry_vdw_other0.232
r_nbd_other0.228
r_nbtor_refined0.193
r_xyhbond_nbd_other0.154
r_chiral_restr0.147
r_symmetry_vdw_refined0.128
r_nbtor_other0.095
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10424
Nucleic Acid Atoms
Solvent Atoms2221
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling