CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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Components
#1: Protein
Putativeserine-pyruvateaminotransferase
Mass: 42173.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter arcticus 273-4 (bacteria) Strain: DSM 17307 / 273-4 / Gene: agxT, Psyc_0177 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q4FVA8
Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH THE 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: 2.18 Å3/Da / Density % sol: 43.46 %
Resolution: 2.2→29.867 Å / Num. obs: 19035 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.162 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 8.8
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.2-2.26
3.7
0.652
1.2
5143
1388
0.652
99.9
2.26-2.32
3.7
0.635
1.1
5071
1364
0.635
99.8
2.32-2.39
3.7
0.508
1.5
4844
1305
0.508
99.9
2.39-2.46
3.7
0.453
1.7
4742
1282
0.453
100
2.46-2.54
3.7
0.405
1.9
4633
1248
0.405
100
2.54-2.63
3.7
0.328
2.3
4499
1209
0.328
100
2.63-2.73
3.7
0.26
2.9
4281
1150
0.26
100
2.73-2.84
3.7
0.239
3.2
4142
1123
0.239
99.9
2.84-2.97
3.7
0.194
3.9
3989
1076
0.194
100
2.97-3.11
3.7
0.145
5.1
3836
1041
0.145
99.9
3.11-3.28
3.7
0.118
6
3688
993
0.118
100
3.28-3.48
3.7
0.097
6.9
3383
922
0.097
100
3.48-3.72
3.7
0.088
6.9
3251
880
0.088
100
3.72-4.02
3.7
0.075
8.2
2992
817
0.075
99.9
4.02-4.4
3.7
0.07
8.3
2803
765
0.07
99.9
4.4-4.92
3.6
0.068
8.8
2517
691
0.068
99.9
4.92-5.68
3.6
0.077
7.9
2186
611
0.077
99.6
5.68-6.96
3.6
0.072
8.7
1877
524
0.072
99.4
6.96-9.84
3.5
0.059
8.9
1462
414
0.059
98.9
9.84-29.87
3.2
0.061
9.7
740
232
0.061
95
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.2→29.867 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.433 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.196 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITY REVEALS RESIDUE LYS-198 TO BE COVALENTLY ATTACHED TO PYRIDOXAL-5'-PHOSPHATE (PLP) VIA A SCHIFF-BASE LINKAGE. THIS COVALENTLY MODIFIED RESIDUE HAS BEEN MODELED AS 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHANE) (LLP). 5. ALTHOUGH CYS 205 HAS BEEN FLAGGED AS A RAMACHANDRAN OUTLIER ITS CURRENT MODELING IS IN AGREEMENT WITH THE ELECTRON DENSITY. 6. ACETATE (ACT), 1,2-ETHANEDIOL (EDO), AND SULFATE (SO4) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 7. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21
983
5.2 %
RANDOM
Rwork
0.167
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-
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obs
0.169
19024
99.77 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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