3AYJ

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 PH7.5, 1.0M AMMONIUM SULFATE, pH 7.50, VAPOR DIFFUSION, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.550.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.985α = 90
b = 112.941β = 90
c = 136.458γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B2SPring-8BL44B2

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
11.129.298.60.0435.3615937
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)
11.11.1697.10.3985.3

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 REPLACEMENTTHROUGHOUT2YR41.129.25849573082798.50.1120.1110.131RANDOM11.8
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]
0.410.1-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.276
r_dihedral_angle_4_deg22.252
r_sphericity_free19.062
r_dihedral_angle_3_deg11.623
r_sphericity_bonded7.176
r_dihedral_angle_1_deg6.525
r_scangle_it5.854
r_scbond_it4.628
r_mcangle_it3.15
r_mcbond_it2.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.276
r_dihedral_angle_4_deg22.252
r_sphericity_free19.062
r_dihedral_angle_3_deg11.623
r_sphericity_bonded7.176
r_dihedral_angle_1_deg6.525
r_scangle_it5.854
r_scbond_it4.628
r_mcangle_it3.15
r_mcbond_it2.64
r_rigid_bond_restr2.306
r_angle_refined_deg2.154
r_angle_other_deg1.141
r_mcbond_other0.848
r_symmetry_vdw_refined0.38
r_symmetry_hbond_refined0.309
r_nbd_refined0.267
r_symmetry_vdw_other0.249
r_xyhbond_nbd_refined0.239
r_nbd_other0.225
r_nbtor_refined0.191
r_chiral_restr0.134
r_nbtor_other0.092
r_xyhbond_nbd_other0.037
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.005
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 Atoms2337
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling