Crystal structure of Putative aromatic amino acid beta-eliminating lyase/threonine aldolase. (YP_001813866.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution
Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: FLAT MIRROR (VERTICAL FOCUSING)
Radiation
Monochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97874 Å / Relative weight: 1
Reflection twin
Crystal-ID
ID
Operator
Domain-ID
Fraction
1
1
H, K, L
1
0.537
1
1
K, H, -L
2
0.463
Reflection
Resolution: 2→46.53 Å / Num. obs: 156755 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.92
Reflection shell
Resolution: 2→2.05 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2→46.53 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.669 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE STRUCTURE WAS PHASED AND TRACED IN APPARENT SPACE GROUP P3121 AND REFINED IN P31 DUE TO TWINNING. TWINNING FACTOR WAS REFINED TO 0.46 FOR TWINNING OPERATOR (K, H, -L). FREE REFLECTIONS WERE EXPANDED BY THE TWIN LAW. 4. PYRIDOXAL-5'-PHOSPHATE (PLP) IS COVALENTLY ATTACHED TO LYSINE 205 VIA A SCHIFF-BASE LINKAGE AND IS MODELED AS LLP.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19
7779
5 %
RANDOM + TWIN LAW
Rwork
0.144
-
-
-
obs
0.146
156744
99.8 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.51 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.73 Å2
0 Å2
0 Å2
2-
-
3.73 Å2
0 Å2
3-
-
-
-7.46 Å2
Refinement step
Cycle: LAST / Resolution: 2→46.53 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
16931
0
0
1339
18270
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
17341
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
11662
X-RAY DIFFRACTION
r_angle_refined_deg
1.543
1.967
23560
X-RAY DIFFRACTION
r_angle_other_deg
1.029
3
28345
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.707
5
2199
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.699
23.962
848
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.75
15
2842
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.019
15
118
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
2540
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
19710
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
3660
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.164
3
10649
X-RAY DIFFRACTION
r_mcbond_other
0.63
3
4402
X-RAY DIFFRACTION
r_mcangle_it
1.955
5
17053
X-RAY DIFFRACTION
r_scbond_it
3.724
8
6692
X-RAY DIFFRACTION
r_scangle_it
5.477
11
6469
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
2028
tightpositional
0.19
0.3
2
B
2028
tightpositional
0.23
0.3
3
C
2028
tightpositional
0.2
0.3
4
D
2028
tightpositional
0.26
0.3
5
E
2028
tightpositional
0.22
0.3
6
F
2028
tightpositional
0.2
0.3
1
A
2413
mediumpositional
0.29
0.6
2
B
2413
mediumpositional
0.31
0.6
3
C
2413
mediumpositional
0.31
0.6
4
D
2413
mediumpositional
0.31
0.6
5
E
2413
mediumpositional
0.31
0.6
6
F
2413
mediumpositional
0.32
0.6
1
A
2028
tightthermal
0.4
0.75
2
B
2028
tightthermal
0.38
0.75
3
C
2028
tightthermal
0.36
0.75
4
D
2028
tightthermal
0.44
0.75
5
E
2028
tightthermal
0.38
0.75
6
F
2028
tightthermal
0.44
0.75
1
A
2413
mediumthermal
0.32
1.5
2
B
2413
mediumthermal
0.31
1.5
3
C
2413
mediumthermal
0.32
1.5
4
D
2413
mediumthermal
0.35
1.5
5
E
2413
mediumthermal
0.3
1.5
6
F
2413
mediumthermal
0.34
1.5
LS refinement shell
Resolution: 2→2.05 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.27
533
-
Rwork
0.162
10895
-
obs
-
-
98.53 %
+
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