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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YR4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	297	0.1M HEPES PH7.5, 1.0M AMMONIUM SULFATE, pH 7.50, VAPOR DIFFUSION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.72

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2		SPring-8	BL44B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.1	29.2	98.6	0.043		5.3		615937

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	97.1		0.398		5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YR4	1.1	29.2	584957	30827	98.5	0.112	0.111	0.12	0.131	0.14	RANDOM	11.8

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]
0.41			0.1		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.276
r_dihedral_angle_4_deg	22.252
r_sphericity_free	19.062
r_dihedral_angle_3_deg	11.623
r_sphericity_bonded	7.176
r_dihedral_angle_1_deg	6.525
r_scangle_it	5.854
r_scbond_it	4.628
r_mcangle_it	3.15
r_mcbond_it	2.64
r_rigid_bond_restr	2.306
r_angle_refined_deg	2.154
r_angle_other_deg	1.141
r_mcbond_other	0.848
r_symmetry_vdw_refined	0.38
r_symmetry_hbond_refined	0.309
r_nbd_refined	0.267
r_symmetry_vdw_other	0.249
r_xyhbond_nbd_refined	0.239
r_nbd_other	0.225
r_nbtor_refined	0.191
r_chiral_restr	0.134
r_nbtor_other	0.092
r_xyhbond_nbd_other	0.037
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	10424
Nucleic Acid Atoms
Solvent Atoms	2337
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling