CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.
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Components
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Protein , 1 types, 1 molecules A
#1: Protein
Succinyl-diaminopimelatedesuccinylase
Mass: 53311.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: dapE, lpg0809 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5ZXC3
Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
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Details
Has protein modification
Y
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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20.00% polyethylene glycol 6000, 1.00M lithium chloride, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97922 Å / Relative weight: 1
Reflection
Resolution: 1.5→29.767 Å / Num. all: 87563 / Num. obs: 87563 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.089 Å2 / Rsym value: 0.098 / Net I/σ(I): 8.5
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
1.5-1.54
4.9
0.772
1
31065
6386
0.772
100
1.54-1.58
4.9
0.625
1.2
30108
6193
0.625
100
1.58-1.63
4.9
0.524
1.5
29660
6079
0.524
100
1.63-1.68
4.9
0.421
1.8
28736
5879
0.421
100
1.68-1.73
4.9
0.353
2.2
28068
5732
0.353
100
1.73-1.79
4.9
0.289
2.7
27174
5537
0.289
100
1.79-1.86
4.9
0.224
3.4
26438
5367
0.224
100
1.86-1.94
4.9
0.183
4.1
25227
5124
0.183
100
1.94-2.02
4.9
0.144
5.1
24560
4979
0.144
100
2.02-2.12
4.9
0.126
5.7
23473
4767
0.126
100
2.12-2.24
4.9
0.114
6.2
22185
4500
0.114
100
2.24-2.37
4.9
0.107
6.4
21176
4288
0.107
100
2.37-2.54
4.9
0.104
6.5
19906
4026
0.104
100
2.54-2.74
4.9
0.09
7.7
18496
3765
0.09
100
2.74-3
4.9
0.076
8.9
17354
3514
0.076
100
3-3.35
4.9
0.07
9.2
15492
3159
0.07
100
3.35-3.87
4.9
0.063
9.9
13721
2822
0.063
100
3.87-4.74
4.8
0.054
11.8
11569
2403
0.054
100
4.74-6.71
4.7
0.061
10.5
8980
1922
0.061
100
6.71-29.767
4.3
0.064
9.7
4838
1121
0.064
98.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
SHELX
phasing
REFMAC
5.5.0110
refinement
SCALA
3.3.15
datascaling
PDB_EXTRACT
3.1
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.5→29.767 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.029 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Phase error: 0.056 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CHLORIDE (CL) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.GLYCEROL (GOL) FROM THE CRYOPROTECTANT AND IMIDAZOLE (IMD) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 7.ZINC (ZN) HAS BEEN MODELED BASED ON AN ANOMALOUS DIFFERENCE FOURIER MAP AND X-RAY FLUORESCENCE EXCITATION SCAN.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.163
4389
5 %
RANDOM
Rwork
0.1376
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obs
0.1389
87480
99.99 %
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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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