A: Phenylacetate-coenzyme A ligase B: Phenylacetate-coenzyme A ligase C: Phenylacetate-coenzyme A ligase D: Phenylacetate-coenzyme A ligase hetero molecules
Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THE CONSTRUCT (RESIDUES 1-435) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-435) 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 16.0% polyethylene glycol 3000, 0.25M sodium chloride, 0.1M HEPES pH 7.9, 5mM Phenylacetate, 5mM MgCl2, 3mM Coenzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2010 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97954 Å / Relative weight: 1
Reflection
Resolution: 2.48→48.889 Å / Num. obs: 69731 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.47 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.33
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.48-2.57
0.724
2.2
34167
6980
99.2
2.57-2.67
0.541
2.9
33549
6714
100
2.67-2.79
0.402
3.8
34063
6827
99.9
2.79-2.94
0.281
5.3
35205
7040
99.9
2.94-3.12
0.208
7
34041
6843
99.9
3.12-3.36
0.121
10.9
34419
6932
99.9
3.36-3.7
0.075
16
34661
7044
99.6
3.7-4.23
0.051
21.6
33989
6978
99.4
4.23-5.31
0.046
25.2
33778
6993
99.1
5.31
0.048
27.1
33878
7380
97.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHARP
phasing
XSCALE
July4, 2012BUILT=20130617
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: SAD / Resolution: 2.48→48.889 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1.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 ...Details: 1.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. 2.PROTEIN ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION. 4. THE MODELING OF ZINC IS IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS AND SIMILAR CRYSTALS OF THE SAME PROTEIN. 5. SODIUM (NA) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 6. ADENOSINE-5'-MONOSPHATE (AMP),MOST LIKELY BOUND TO THE PROTEIN DURING EXPRESSION WAS MODELED INTO THE ACTIVE SITE ON SUBUNITS A,B, AND D IN THE ASYMMETRIC UNIT. HOWEVER,ELECTRON DENSITY FOR AMP WAS ABSENT ON SUBUNIT C; THEREFORE AMO COULD NOT BE RELIABLY MODELED INTO THE ACTIVE SITE OF THIS SUBUNIT. 7. ASN 243 ON THE A,B,C, AND D-CHAINS ARE RAMACHANDRAN OUTLIERS IN MOLPROBITY EVEN THOUGH THEIR POSITIONINGS ARE SUPPORTED BY ELECTRON DENSITY. LYS 84 ON THE C-CHAIN IS A RAMACHANDRAN OUTLIER EVEN THOUGH ITS POSITIONING IS SUPPORTED BY ELECTRON DENSITY. SER 382 AND ASN 367 ON THE B CHAIN, AND VAL 366 ON THE D CHAIN ARE IN POOR REGIONS OF ELECTRON DENSITY AND ARE FLAGGED AS RAMACHANDRAN OUTLIERS IN MOLPROBITY.
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