ANALYTICAL SIZE EXCLUSION CHROMATOGRPAHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN HAS ASSOCIATED INTO TRIMERS THAT ARE PREDICTED TO BE STABLE.
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Components
#1: Protein
Peptidyl-prolylcis-transisomeraseE / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E
Mass: 19319.230 Da / Num. of mol.: 1 / Fragment: residues 129-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BC008451, CYP33, PPIE / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9UNP9, peptidylprolyl isomerase
Mass: 18.015 Da / Num. of mol.: 49 / 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 RESIDUES 129-301 OF THE TARGET SEQUENCE. THE SEQUENCE NUMBERING CORRESPONDS TO ISOFORM A (UNIPROTKB ID Q9UNP9-1)
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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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20.0% PEG-1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97894 Å / Relative weight: 1
Reflection
Resolution: 2.5→29.058 Å / Num. all: 9184 / Num. obs: 9184 / % possible obs: 99.9 % / Redundancy: 23.2 % / Rsym value: 0.149 / Net I/σ(I): 17.2
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
2.5-2.57
12
0.801
2.7
7119
593
0.801
100
2.57-2.64
23.7
1.168
4.3
15292
646
1.168
100
2.64-2.71
24.2
1.024
5.1
15869
655
1.024
100
2.71-2.8
24.4
0.677
6.5
15157
622
0.677
100
2.8-2.89
24.3
0.454
9
14774
608
0.454
100
2.89-2.99
24.2
0.345
10.8
14302
590
0.345
100
2.99-3.1
24.2
0.284
12.8
13458
555
0.284
100
3.1-3.23
24.3
0.221
16.3
13203
543
0.221
100
3.23-3.37
24.2
0.188
19.8
12710
526
0.188
100
3.37-3.54
24.1
0.151
22.2
12008
499
0.151
100
3.54-3.73
24.2
0.133
24.6
11624
481
0.133
100
3.73-3.95
23.9
0.114
26.1
10920
457
0.114
100
3.95-4.23
24
0.113
27.9
10260
428
0.113
100
4.23-4.57
23.9
0.099
31
9540
399
0.099
100
4.57-5
23.6
0.116
31.3
8793
373
0.116
100
5-5.59
23.6
0.124
30
7858
333
0.124
100
5.59-6.46
23.3
0.114
29.7
6904
296
0.114
100
6.46-7.91
23
0.105
30.7
6040
263
0.105
100
7.91-11.18
22.5
0.088
34.5
4577
203
0.088
100
11.18-29.058
20.2
0.089
31.4
2303
114
0.089
94.2
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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
SHELX
phasing
SHARP
phasing
SCALA
3.3.15
datascaling
REFMAC
5.5.0110
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.5→29.058 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.617 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2142
437
4.8 %
RANDOM
Rwork
0.1901
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-
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obs
0.1912
9184
100 %
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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: BABINET MODEL WITH MASK
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