AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS FORMING A DIMER. CRYSTAL PACKING ANALYSIS SUGGESTS THAT THIS IS THE STABLE OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
L-tyrosinedecarboxylaseMfnA / TDC
Mass: 45596.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: mfnA, MJ0050, NP_247014.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q60358, tyrosine decarboxylase
Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40.0000% MPD, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
Radiation
Monochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97952 Å / Relative weight: 1
Reflection
Resolution: 2.11→29.975 Å / Num. obs: 62121 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.594 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 3.203
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
2.11-2.16
4.6
0.772
1
20882
4543
0.772
100
2.16-2.22
4.6
0.583
1.3
20283
4411
0.583
100
2.22-2.29
4.6
0.509
1.4
19744
4293
0.509
100
2.29-2.36
4.6
0.441
1.7
19291
4198
0.441
100
2.36-2.44
4.6
0.372
2
18739
4067
0.372
100
2.44-2.52
4.6
0.299
2.5
17977
3915
0.299
100
2.52-2.62
4.6
0.253
2.9
17542
3814
0.253
100
2.62-2.72
4.6
0.207
3.5
16765
3646
0.207
100
2.72-2.85
4.6
0.173
4.3
16251
3523
0.173
100
2.85-2.98
4.6
0.145
5
15360
3355
0.145
100
2.98-3.15
4.6
0.136
5.2
14662
3216
0.136
100
3.15-3.34
4.5
0.111
6.1
13845
3044
0.111
100
3.34-3.57
4.5
0.091
7
12938
2859
0.091
100
3.57-3.85
4.5
0.077
8.4
12163
2687
0.077
100
3.85-4.22
4.5
0.072
3.3
11166
2468
0.072
100
4.22-4.72
4.5
0.07
8.7
10079
2250
0.07
100
4.72-5.45
4.4
0.081
7.5
8895
2008
0.081
100
5.45-6.67
4.4
0.081
7.7
7477
1715
0.081
100
6.67-9.44
4.3
0.071
6.3
5816
1353
0.071
99.9
9.44-29.975
4
0.082
3.9
3004
756
0.082
96
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: SAD / Resolution: 2.11→29.975 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.222 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.14 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.2,4-METHYL PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 5.PYRIDOXAL PHOSPHATE (PLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF BOTH PROTOMERS BASED ON CLEAR AND UNAMBIGUOUS ELECTRON DENSITY IN THE EXPERIMENTALLY PHASED MAPS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.192
3141
5.1 %
RANDOM
Rwork
0.158
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-
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obs
0.16
62056
99.93 %
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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
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