Mass: 115762.133 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1104, MP1, PITRM1 / Plasmid: pProExH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#4: Protein
Presequenceprotease, mitochondrial / Beta-APP40
Mass: 115572.414 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JRX3
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Beta-amyloid protein ... , 2 types, 4 molecules BECF
#2: Protein/peptide
Beta-amyloidprotein40 / Amyloid beta / Beta-APP40
Mass: 4335.852 Da / Num. of mol.: 2 / Fragment: UNP residues 572-711 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
I328V, A397V, AND Q1037R IN CHAINS A AND D ARE NATURAL VARIANTS. CHAINS C AND F ARE IDENTICAL TO ...I328V, A397V, AND Q1037R IN CHAINS A AND D ARE NATURAL VARIANTS. CHAINS C AND F ARE IDENTICAL TO CHAINS B AND E, BUT THE IDENTITIES OF THE MODELED RESIDUES ARE NOT KNOWN.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal grow
Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution: 2.7→2.75 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 3557 / Rsym value: 0.597 / % possible all: 98.2
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
PHASER
phasing
PHENIX
(phenix.refine: 1.8.2_1309)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: molecular replacement/SAD / Resolution: 2.704→39.621 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: MLHL Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS (CHAINS A AND D) WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS (CHAINS A AND D) WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2323
3724
4.96 %
RANDOM
Rwork
0.1908
-
-
-
obs
0.193
67540
88 %
-
all
-
72669
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 44.63 Å2
Refinement step
Cycle: LAST / Resolution: 2.704→39.621 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
15966
0
28
40
16034
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
16415
X-RAY DIFFRACTION
f_angle_d
1.024
22252
X-RAY DIFFRACTION
f_dihedral_angle_d
13.106
6175
X-RAY DIFFRACTION
f_chiral_restr
0.032
2419
X-RAY DIFFRACTION
f_plane_restr
0.004
2879
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.704-2.7379
0.3193
79
0.2283
1743
X-RAY DIFFRACTION
35
2.7379-2.774
0.2717
96
0.2251
1886
X-RAY DIFFRACTION
37
2.774-2.8119
0.3334
102
0.2225
1928
X-RAY DIFFRACTION
39
2.8119-2.8521
0.2996
104
0.2236
2077
X-RAY DIFFRACTION
41
2.8521-2.8947
0.3167
112
0.2281
2095
X-RAY DIFFRACTION
42
2.8947-2.9399
0.305
120
0.2264
2121
X-RAY DIFFRACTION
43
2.9399-2.9881
0.3084
119
0.2202
2229
X-RAY DIFFRACTION
44
2.9881-3.0396
0.3409
113
0.2257
2261
X-RAY DIFFRACTION
45
3.0396-3.0948
0.275
117
0.2126
2326
X-RAY DIFFRACTION
47
3.0948-3.1543
0.2753
138
0.2151
2379
X-RAY DIFFRACTION
48
3.1543-3.2187
0.2826
121
0.2107
2455
X-RAY DIFFRACTION
49
3.2187-3.2886
0.2622
141
0.2008
2445
X-RAY DIFFRACTION
50
3.2886-3.3651
0.2211
127
0.2025
2519
X-RAY DIFFRACTION
50
3.3651-3.4492
0.2392
125
0.197
2561
X-RAY DIFFRACTION
50
3.4492-3.5424
0.2325
134
0.1991
2490
X-RAY DIFFRACTION
51
3.5424-3.6466
0.2573
127
0.1926
2579
X-RAY DIFFRACTION
51
3.6466-3.7642
0.2397
142
0.1906
2556
X-RAY DIFFRACTION
51
3.7642-3.8986
0.2093
139
0.1901
2579
X-RAY DIFFRACTION
52
3.8986-4.0546
0.2321
131
0.1738
2613
X-RAY DIFFRACTION
52
4.0546-4.2389
0.2252
147
0.1702
2645
X-RAY DIFFRACTION
53
4.2389-4.4621
0.2071
142
0.1602
2695
X-RAY DIFFRACTION
54
4.4621-4.7412
0.2013
143
0.1521
2825
X-RAY DIFFRACTION
57
4.7412-5.1066
0.1953
169
0.1643
3089
X-RAY DIFFRACTION
62
5.1066-5.6192
0.2115
168
0.1908
3637
X-RAY DIFFRACTION
72
5.6192-6.4293
0.226
215
0.2058
4097
X-RAY DIFFRACTION
82
6.4293-8.0889
0.2214
223
0.2031
4372
X-RAY DIFFRACTION
87
8.0889-39.625
0.1935
230
0.1808
4129
X-RAY DIFFRACTION
83
+
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