SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN IS MONOMERIC. THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY.
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Components
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Protein , 1 types, 2 molecules AB
#1: Protein
PutativesulfataseyidJ
Mass: 54342.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, DSM 2079, NCTC 10582 / Gene: NP_810509.1, BT_1596 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A7C8
Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 20.0% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2007 / Details: Adjustable focusing mirrors in K-B geometry
Radiation
Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97942 Å / Relative weight: 1
Reflection
Resolution: 2.4→29.907 Å / Num. obs: 47977 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 40.49 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.4-2.46
3.8
0.673
1
13362
3478
0.673
98.6
2.46-2.53
3.9
0.535
1.3
13356
3460
0.535
98.5
2.53-2.6
3.8
0.471
1.5
12828
3340
0.471
99
2.6-2.68
4
0.43
1.6
12813
3236
0.43
99.1
2.68-2.77
6.8
0.594
1.1
21257
3133
0.594
98.9
2.77-2.87
6.8
0.453
1.4
20873
3069
0.453
98.8
2.87-2.98
6.9
0.365
1.8
20246
2951
0.365
99.4
2.98-3.1
6.9
0.284
2.4
19559
2830
0.284
98.9
3.1-3.24
7
0.227
3
19098
2724
0.227
99.5
3.24-3.39
7.1
0.179
3.9
18680
2624
0.179
99.1
3.39-3.58
7.2
0.137
5.1
18018
2499
0.137
99.6
3.58-3.79
7.4
0.117
5.9
17276
2346
0.117
99.2
3.79-4.06
7.4
0.101
6.8
16483
2227
0.101
99.5
4.06-4.38
7.5
0.093
7.3
15303
2051
0.093
99.5
4.38-4.8
7.4
0.089
7.6
14191
1913
0.089
99.7
4.8-5.37
7.4
0.084
7.8
12712
1723
0.084
99.5
5.37-6.2
7.3
0.092
7.3
11165
1526
0.092
99.8
6.2-7.59
7.2
0.093
7
9256
1287
0.093
99.7
7.59-10.73
7
0.067
9.5
7178
1021
0.067
99.8
10.73-29.907
6.7
0.066
8.6
3618
539
0.066
95.3
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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
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.4→29.907 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.979 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.209 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ZINC HAS BEEN MODELED IN THE STRUCTURE BASED ON AN ANOMALOUS DIFFERENCE FOURIER ELECTRON DENSITY MAP AND COORDINATION GEOMETRY. 4. 1,2-ETHANEDIOL, HEPES AND PARTIAL PEG MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. THERE ARE THREE RAMACHANDRAN OUTLIERS AT POSITIONS A166, B168 AND B297.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.206
2420
5 %
RANDOM
Rwork
0.149
-
-
-
obs
0.152
47974
99.17 %
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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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