0.026203 0.015128 0.000000 0.000000 0.030256 0.000000 0.000000 0.000000 0.031197 0.00000 0.00000 0.00000 0000-0002-9724-6298 Kreutzer, A.G. 0000-0003-4739-0619 Ruttenberg, S.M. 0000-0002-2273-1029 Nowick, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 38.164 38.164 32.054 C3 H7 N O2 89.093 y ALANINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C7 H15 N O2 145.199 n N-METHYL-ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C5 H12 N2 O2 132.161 n L-ornithine L-peptide linking C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C2 H F3 O2 114.023 trifluoroacetic acid non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N O N 21 N O N 22 N O N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N N N 31 S C N 32 N C N 33 N O N 34 N C N 35 N C N 36 N C N 37 N O N 38 N O N 39 N O N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N N N 50 N C N 51 N C N 52 N O N 53 N O N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N O N 60 N H N 61 N H N 62 N N N 63 S C N 64 N C N 65 N O N 66 S C N 67 N C N 68 N C N 69 N C N 70 N O N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N N N 85 S C N 86 N C N 87 N O N 88 N O N 89 S C N 90 N C N 91 N C N 92 N C N 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N N N 110 S C N 111 N C N 112 N O N 113 N C N 114 N C N 115 N C N 116 N C N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N C N 137 N S N 138 N C N 139 N O N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N N N 152 S C N 153 N C N 154 N C N 155 N C N 156 N N N 157 N C N 158 N O N 159 N O N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N C N 173 N O N 174 N C N 175 N O N 176 N C N 177 N C N 178 N O N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N N N 190 S C N 191 N C N 192 N O N 193 N C Y 194 N C Y 195 N C Y 196 N C Y 197 N C Y 198 N C Y 199 N C N 200 N O N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N C N 213 N C N 214 N O N 215 N F N 216 N F N 217 N F N 218 N O N 219 N H N 220 N N N 221 S C N 222 N C N 223 N O N 224 N C N 225 N C N 226 N C N 227 N O N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N doub N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N doub N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N doub N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing Y 189 N doub Y 190 N sing Y 191 N sing N 192 N sing Y 193 N doub N 194 N sing Y 195 N doub N 196 N sing Y 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N doub N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing US Biochemistry BICHAW 0033 0006-2960 63 212 218 10.1021/acs.biochem.3c00526 38163326 beta-Hairpin Alignment Alters Oligomer Formation in A beta-Derived Peptides. 2024 10.2210/pdb8gjc/pdb pdb_00008gjc 103.15 1 N PIXEL 2022-04-21 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 0.99999 1.0 5.0.2 ALS 0.99999 SYNCHROTRON ALS BEAMLINE 5.0.2 1606.903 beta-hairpin peptide derived from Abeta 17-35 2 syn polymer 149.211 METHIONINE 2 syn non-polymer 114.023 trifluoroacetic acid 3 syn non-polymer 106.120 DI(HYDROXYETHYL)ETHER 1 syn non-polymer 18.015 water 31 nat water (ORN)LVFFAED(ORN)GAI(N-Me-Ile)GLM no yes (ORN)LVFFAED(ORN)GAI(IML)GL ALVFFAEDAGAIIGL A,B polypeptide(L) n n n n n n n n n n n n n n n 1 2.10 41.34 VAPOR DIFFUSION, HANGING DROP Molecular Dynamics Morpheus solution containing 0.12M ethylene glycols mix, 0.1M Buffer System 3 pH 8.5, and 37.5% v/v precipitant mix 4. Molecular Dynamics ethylene glycols mix consists of 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M penta(ethylene glycol). Molecular Dynamics Buffer System 3 consists of 1 M BICINE and 1 M Trisma Base. Molecular Dynamics precipitant mix 4 consists of 25 % w/v hexylene glycol, 25 % w/v poly(ethylene glycol) 1000, and 25 % w/v poly(ethylene glycol) 3350. 298.15 citation citation_author repository Initial release Database references 1 0 2024-01-17 1 1 2024-01-31 _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID United States National Institutes of Health/National Institute on Aging (NIH/NIA) AG072587 jsnowick@uci.edu 0000-0002-2273-1029 James Nowick S principal investigator/group leader N RCSB Y RCSB 2023-03-15 REL REL 1 A O HOH 217 6.73 MET METHIONINE TFA trifluoroacetic acid PEG DI(HYDROXYETHYL)ETHER HOH water 32630 synthetic construct sample 1 15 N 5W4H PDB experimental model MET 16 2 MET MET 101 A TFA 1 3 TFA TFA 102 A TFA 2 3 TFA TFA 103 A MET 16 2 MET MET 101 B TFA 3 3 TFA TFA 102 B PEG 1 4 PEG PEG 103 B HOH 24 5 HOH HOH 201 A HOH 30 5 HOH HOH 202 A HOH 27 5 HOH HOH 203 A HOH 5 5 HOH HOH 204 A HOH 4 5 HOH HOH 205 A HOH 12 5 HOH HOH 206 A HOH 14 5 HOH HOH 207 A HOH 31 5 HOH HOH 208 A HOH 3 5 HOH HOH 209 A HOH 6 5 HOH HOH 210 A HOH 7 5 HOH HOH 211 A HOH 8 5 HOH HOH 212 A HOH 10 5 HOH HOH 213 A HOH 16 5 HOH HOH 214 A HOH 13 5 HOH HOH 215 A HOH 26 5 HOH HOH 216 A HOH 29 5 HOH HOH 217 A HOH 18 5 HOH HOH 201 B HOH 25 5 HOH HOH 202 B HOH 11 5 HOH HOH 203 B HOH 19 5 HOH HOH 204 B HOH 1 5 HOH HOH 205 B HOH 20 5 HOH HOH 206 B HOH 21 5 HOH HOH 207 B HOH 28 5 HOH HOH 208 B HOH 15 5 HOH HOH 209 B HOH 22 5 HOH HOH 210 B HOH 9 5 HOH HOH 211 B HOH 2 5 HOH HOH 212 B HOH 23 5 HOH HOH 213 B HOH 17 5 HOH HOH 214 B ORN 1 n 1 ORN 1 A LEU 2 n 2 LEU 2 A VAL 3 n 3 VAL 3 A PHE 4 n 4 PHE 4 A PHE 5 n 5 PHE 5 A ALA 6 n 6 ALA 6 A GLU 7 n 7 GLU 7 A ASP 8 n 8 ASP 8 A ORN 9 n 9 ORN 9 A GLY 10 n 10 GLY 10 A ALA 11 n 11 ALA 11 A ILE 12 n 12 ILE 12 A IML 13 n 13 IML 13 A GLY 14 n 14 GLY 14 A LEU 15 n 15 LEU 15 A ORN 1 n 1 ORN 1 B LEU 2 n 2 LEU 2 B VAL 3 n 3 VAL 3 B PHE 4 n 4 PHE 4 B PHE 5 n 5 PHE 5 B ALA 6 n 6 ALA 6 B GLU 7 n 7 GLU 7 B ASP 8 n 8 ASP 8 B ORN 9 n 9 ORN 9 B GLY 10 n 10 GLY 10 B ALA 11 n 11 ALA 11 B ILE 12 n 12 ILE 12 B IML 13 n 13 IML 13 B GLY 14 n 14 GLY 14 B LEU 15 n 15 LEU 15 B author_and_software_defined_assembly PISA 4 tetrameric none 2800 -23 5040 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_555 y,x,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 A N PHE 4 A N PHE 4 A O GLY 14 A O GLY 14 B N PHE 4 B N PHE 4 B O GLY 14 B O GLY 14 1 A HOH 217 I HOH 1 A A C N LEU MET 15 101 1.33 1 B B C N LEU MET 15 101 1.33 1 B B O O HOH HOH 204 206 2.02 1 A B O O HOH HOH 214 214 2.03 1 B B O O HOH HOH 208 210 2.06 1 A B O O HOH HOH 208 213 1.85 1_555 6_665 1 A A O O HOH HOH 216 216 1.86 1_555 4_555 1 B B O O HOH HOH 206 208 1.91 1_555 4_556 1 B B O O HOH HOH 204 208 1.93 1_555 4_556 0.1807 0.1547 0.1597 1.431 23.01 952 9354 10.18 96.91 1 FREE R-VALUE 7.36 MOLECULAR REPLACEMENT 20.89 0.90 1.10 5W4H TWIN_LSQ_F FLAT BULK SOLVENT MODEL 1.431 23.01 31 301 44 0 226 0.006 1.146 36.081 72 0.080 38 0.005 43 0.5178 0.5055 1.51 107 994 72.00 0.3736 0.3070 1.60 145 1228 88.00 0.2298 0.1921 1.72 132 1241 90.00 0.1695 0.1597 1.90 140 1229 90.00 0.1660 0.1517 2.17 140 1241 90.00 0.1889 0.1291 2.74 127 1253 91.00 0.1381 0.1276 23.01 141 1236 90.00 1.431 23.01 8GJC 9354 0.999 0.09013 1 24.44 16.0 97.02 1.775 1.431 1.482 384 0.25 1 refinement PHENIX 1.20.1_4487 data reduction XDS data scaling Aimless phasing PHENIX N X-ray crystallographic structure of a beta-hairpin peptide derived from Abeta 17-35. (ORN)LVFFAED(ORN)GAI(N-Me-Ile)GLM 1 N N 1 N N 2 N N 3 N N 3 N N 2 N N 3 N N 4 N N 5 N N 5 N N covale 1.370 both A ORN 1 A C ORN 1 1_555 A LEU 2 A N LEU 2 1_555 covale 1.376 both A ORN 1 A NE ORN 1 1_555 A MET 101 C C MET 1_555 covale 1.377 both A ASP 8 A C ASP 8 1_555 A ORN 9 A NE ORN 9 1_555 covale 1.369 both A ORN 9 A C ORN 9 1_555 A GLY 10 A N GLY 10 1_555 covale 1.334 both A ILE 12 A C ILE 12 1_555 A IML 13 A N IML 13 1_555 covale 1.327 both A IML 13 A C IML 13 1_555 A GLY 14 A N GLY 14 1_555 covale 1.372 both B ORN 1 B C ORN 1 1_555 B LEU 2 B N LEU 2 1_555 covale 1.372 both B ORN 1 B NE ORN 1 1_555 B MET 101 F C MET 1_555 covale 1.374 both B ASP 8 B C ASP 8 1_555 B ORN 9 B NE ORN 9 1_555 covale 1.368 both B ORN 9 B C ORN 9 1_555 B GLY 10 B N GLY 10 1_555 covale 1.331 both B ILE 12 B C ILE 12 1_555 B IML 13 B N IML 13 1_555 covale 1.329 both B IML 13 B C IML 13 1_555 B GLY 14 B N GLY 14 1_555 DE NOVO PROTEIN oligomer, tetramer, amyloid, Alzheimer's disease, DE NOVO PROTEIN 8GJC PDB 1 1 8GJC 1 15 8GJC 1 15 8GJC A 1 1 15 1 15 8GJC 1 15 8GJC B 1 1 15 2 2 anti-parallel anti-parallel A PHE 4 A PHE 4 A GLU 7 A GLU 7 A ALA 11 A ALA 11 A GLY 14 A GLY 14 B PHE 4 B PHE 4 B GLU 7 B GLU 7 B ALA 11 B ALA 11 B GLY 14 B GLY 14 154 P 32 2 1