0.010249 0.000000 0.000000 0.000000 0.010249 0.000000 0.000000 0.000000 0.014602 0.00000 0.00000 0.00000 Fernandez-Tornero, C. Garcia, E. Lopez, R. Gimenez-Gallego, G. Romero, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 97.571 97.571 68.482 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H14 N O 1 104.171 CHOLINE ION non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE 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 C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Nat.Struct.Biol. NSBIEW 2024 1072-8368 8 1020 10.1038/NSB724 11694890 A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factor Lyta 2001 NE Gene GENED6 0861 0378-1119 89 69 10.1016/0378-1119(90)90207-8 1973677 Cloning and Expression of Gene Fragments Encoding the Choline-Binding Domain of Pneumococcal Murein Hydrolases 1990 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 MIRRORS CCD 2000-07-15 MARRESEARCH GE SINGLE WAVELENGTH M x-ray 1 0.9073 1.0 X11 EMBL/DESY, HAMBURG 0.9073 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 11153.843 MAJOR AUTOLYSIN 3.5.1.28 CHOLINE-BINDING DOMAIN 2 man polymer 104.171 CHOLINE ION 6 syn non-polymer 18.015 water 61 nat water C-LYTA, CELL WALL BINDING DOMAIN no yes TDGNWYWFDNSGE(MSE)ATGWKKIADKWYYFNEEGA(MSE)KTGWVKYKDTWYYLDAKEGA(MSE)VSNAFIQSADGTG WYYLKPDGTLADRPEFTVEPDGLITVK TDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLAD RPEFTVEPDGLITVK A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample EXTRACELLULAR LYTA 1313 STREPTOCOCCUS PNEUMONIAE CYTOPLASM 511693 ESCHERICHIA COLI BL21 PLASMID PCE17 1 2.6 52 A FIRST STRUCTURE, WHOSE STATISTICS HAVE NOT BEEN SUBMITTED, WAS DETERMINED TO 3.0 ANGSTROM RESOLUTION THROUGH A MAD EXPERIMENT. A SECOND EXPERIMENT WAS THEN PERFORMED ON A SINGLE CRYSTAL. IT IS STRUCTURE REFINED AGAINST THE DATA FROM THIS SECOND EXPERIMENT THAT IS PRESENTED IN THIS ENTRY 4.60 30% MPD, 0.2 M NACL, 0.1 M NA-ACETATE, PH 4.6, 0.2 M GUANIDINE-HCL, 0.15 M CHOLINE-CL. diffrn_source struct_conn repository Initial release Version format compliance Version format compliance Data collection Derived calculations 1 0 2002-01-31 1 1 2011-05-08 1 2 2011-07-13 1 3 2019-07-24 _diffrn_source.pdbx_synchrotron_site _struct_conn.pdbx_leaving_atom_flag SHEET DETERMINATION METHOD: AUTHOR PROVIDED. PDBE Y PDBE 2001-02-06 REL CHT CHOLINE ION HOH water CHT 401 2 CHT CHT 401 A CHT 402 2 CHT CHT 402 A CHT 403 2 CHT CHT 403 A CHT 404 2 CHT CHT 404 B CHT 405 2 CHT CHT 405 B CHT 406 2 CHT CHT 406 B HOH 2001 3 HOH HOH 2001 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2022 3 HOH HOH 2022 A HOH 2023 3 HOH HOH 2023 A HOH 2024 3 HOH HOH 2024 A HOH 2025 3 HOH HOH 2025 A HOH 2026 3 HOH HOH 2026 A HOH 2001 3 HOH HOH 2001 B HOH 2002 3 HOH HOH 2002 B HOH 2003 3 HOH HOH 2003 B HOH 2004 3 HOH HOH 2004 B HOH 2005 3 HOH HOH 2005 B HOH 2006 3 HOH HOH 2006 B HOH 2007 3 HOH HOH 2007 B HOH 2008 3 HOH HOH 2008 B HOH 2009 3 HOH HOH 2009 B HOH 2010 3 HOH HOH 2010 B HOH 2011 3 HOH HOH 2011 B HOH 2012 3 HOH HOH 2012 B HOH 2013 3 HOH HOH 2013 B HOH 2014 3 HOH HOH 2014 B HOH 2015 3 HOH HOH 2015 B HOH 2016 3 HOH HOH 2016 B HOH 2017 3 HOH HOH 2017 B HOH 2018 3 HOH HOH 2018 B HOH 2019 3 HOH HOH 2019 B HOH 2020 3 HOH HOH 2020 B HOH 2021 3 HOH HOH 2021 B HOH 2022 3 HOH HOH 2022 B HOH 2023 3 HOH HOH 2023 B HOH 2024 3 HOH HOH 2024 B HOH 2025 3 HOH HOH 2025 B HOH 2026 3 HOH HOH 2026 B HOH 2027 3 HOH HOH 2027 B HOH 2028 3 HOH HOH 2028 B HOH 2029 3 HOH HOH 2029 B HOH 2030 3 HOH HOH 2030 B HOH 2031 3 HOH HOH 2031 B HOH 2032 3 HOH HOH 2032 B HOH 2033 3 HOH HOH 2033 B HOH 2034 3 HOH HOH 2034 B HOH 2035 3 HOH HOH 2035 B THR 224 n 1 THR 224 A ASP 225 n 2 ASP 225 A GLY 226 n 3 GLY 226 A ASN 227 n 4 ASN 227 A TRP 228 n 5 TRP 228 A TYR 229 n 6 TYR 229 A TRP 230 n 7 TRP 230 A PHE 231 n 8 PHE 231 A ASP 232 n 9 ASP 232 A ASN 233 n 10 ASN 233 A SER 234 n 11 SER 234 A GLY 235 n 12 GLY 235 A GLU 236 n 13 GLU 236 A MSE 237 n 14 MSE 237 A ALA 238 n 15 ALA 238 A THR 239 n 16 THR 239 A GLY 240 n 17 GLY 240 A TRP 241 n 18 TRP 241 A LYS 242 n 19 LYS 242 A LYS 243 n 20 LYS 243 A ILE 244 n 21 ILE 244 A ALA 245 n 22 ALA 245 A ASP 246 n 23 ASP 246 A LYS 247 n 24 LYS 247 A TRP 248 n 25 TRP 248 A TYR 249 n 26 TYR 249 A TYR 250 n 27 TYR 250 A PHE 251 n 28 PHE 251 A ASN 252 n 29 ASN 252 A GLU 253 n 30 GLU 253 A GLU 254 n 31 GLU 254 A GLY 255 n 32 GLY 255 A ALA 256 n 33 ALA 256 A MSE 257 n 34 MSE 257 A LYS 258 n 35 LYS 258 A THR 259 n 36 THR 259 A GLY 260 n 37 GLY 260 A TRP 261 n 38 TRP 261 A VAL 262 n 39 VAL 262 A LYS 263 n 40 LYS 263 A TYR 264 n 41 TYR 264 A LYS 265 n 42 LYS 265 A ASP 266 n 43 ASP 266 A THR 267 n 44 THR 267 A TRP 268 n 45 TRP 268 A TYR 269 n 46 TYR 269 A TYR 270 n 47 TYR 270 A LEU 271 n 48 LEU 271 A ASP 272 n 49 ASP 272 A ALA 273 n 50 ALA 273 A LYS 274 n 51 LYS 274 A GLU 275 n 52 GLU 275 A GLY 276 n 53 GLY 276 A ALA 277 n 54 ALA 277 A MSE 278 n 55 MSE 278 A VAL 279 n 56 VAL 279 A SER 280 n 57 SER 280 A ASN 281 n 58 ASN 281 A ALA 282 n 59 ALA 282 A PHE 283 n 60 PHE 283 A ILE 284 n 61 ILE 284 A GLN 285 n 62 GLN 285 A SER 286 n 63 SER 286 A ALA 287 n 64 ALA 287 A ASP 288 n 65 ASP 288 A GLY 289 n 66 GLY 289 A THR 290 n 67 THR 290 A GLY 291 n 68 GLY 291 A TRP 292 n 69 TRP 292 A TYR 293 n 70 TYR 293 A TYR 294 n 71 TYR 294 A LEU 295 n 72 LEU 295 A LYS 296 n 73 LYS 296 A PRO 297 n 74 PRO 297 A ASP 298 n 75 ASP 298 A GLY 299 n 76 GLY 299 A THR 300 n 77 THR 300 A LEU 301 n 78 LEU 301 A ALA 302 n 79 ALA 302 A ASP 303 n 80 ASP 303 A ARG 304 n 81 ARG 304 A PRO 305 n 82 PRO 305 A GLU 306 n 83 GLU 306 A PHE 307 n 84 PHE 307 A THR 308 n 85 THR 308 A VAL 309 n 86 VAL 309 A GLU 310 n 87 GLU 310 A PRO 311 n 88 PRO 311 A ASP 312 n 89 ASP 312 A GLY 313 n 90 GLY 313 A LEU 314 n 91 LEU 314 A ILE 315 n 92 ILE 315 A THR 316 n 93 THR 316 A VAL 317 n 94 VAL 317 A LYS 318 n 95 LYS 318 A n 1 224 B ASP 225 n 2 ASP 225 B GLY 226 n 3 GLY 226 B ASN 227 n 4 ASN 227 B TRP 228 n 5 TRP 228 B TYR 229 n 6 TYR 229 B TRP 230 n 7 TRP 230 B PHE 231 n 8 PHE 231 B ASP 232 n 9 ASP 232 B ASN 233 n 10 ASN 233 B SER 234 n 11 SER 234 B GLY 235 n 12 GLY 235 B GLU 236 n 13 GLU 236 B MSE 237 n 14 MSE 237 B ALA 238 n 15 ALA 238 B THR 239 n 16 THR 239 B GLY 240 n 17 GLY 240 B TRP 241 n 18 TRP 241 B LYS 242 n 19 LYS 242 B LYS 243 n 20 LYS 243 B ILE 244 n 21 ILE 244 B ALA 245 n 22 ALA 245 B ASP 246 n 23 ASP 246 B LYS 247 n 24 LYS 247 B TRP 248 n 25 TRP 248 B TYR 249 n 26 TYR 249 B TYR 250 n 27 TYR 250 B PHE 251 n 28 PHE 251 B ASN 252 n 29 ASN 252 B GLU 253 n 30 GLU 253 B GLU 254 n 31 GLU 254 B GLY 255 n 32 GLY 255 B ALA 256 n 33 ALA 256 B MSE 257 n 34 MSE 257 B LYS 258 n 35 LYS 258 B THR 259 n 36 THR 259 B GLY 260 n 37 GLY 260 B TRP 261 n 38 TRP 261 B VAL 262 n 39 VAL 262 B LYS 263 n 40 LYS 263 B TYR 264 n 41 TYR 264 B LYS 265 n 42 LYS 265 B ASP 266 n 43 ASP 266 B THR 267 n 44 THR 267 B TRP 268 n 45 TRP 268 B TYR 269 n 46 TYR 269 B TYR 270 n 47 TYR 270 B LEU 271 n 48 LEU 271 B ASP 272 n 49 ASP 272 B ALA 273 n 50 ALA 273 B LYS 274 n 51 LYS 274 B GLU 275 n 52 GLU 275 B GLY 276 n 53 GLY 276 B ALA 277 n 54 ALA 277 B MSE 278 n 55 MSE 278 B VAL 279 n 56 VAL 279 B SER 280 n 57 SER 280 B ASN 281 n 58 ASN 281 B ALA 282 n 59 ALA 282 B PHE 283 n 60 PHE 283 B ILE 284 n 61 ILE 284 B GLN 285 n 62 GLN 285 B SER 286 n 63 SER 286 B ALA 287 n 64 ALA 287 B ASP 288 n 65 ASP 288 B GLY 289 n 66 GLY 289 B THR 290 n 67 THR 290 B GLY 291 n 68 GLY 291 B TRP 292 n 69 TRP 292 B TYR 293 n 70 TYR 293 B TYR 294 n 71 TYR 294 B LEU 295 n 72 LEU 295 B LYS 296 n 73 LYS 296 B PRO 297 n 74 PRO 297 B ASP 298 n 75 ASP 298 B GLY 299 n 76 GLY 299 B THR 300 n 77 THR 300 B LEU 301 n 78 LEU 301 B ALA 302 n 79 ALA 302 B ASP 303 n 80 ASP 303 B ARG 304 n 81 ARG 304 B PRO 305 n 82 PRO 305 B GLU 306 n 83 GLU 306 B PHE 307 n 84 PHE 307 B THR 308 n 85 THR 308 B VAL 309 n 86 VAL 309 B GLU 310 n 87 GLU 310 B PRO 311 n 88 PRO 311 B ASP 312 n 89 ASP 312 B GLY 313 n 90 GLY 313 B LEU 314 n 91 LEU 314 B ILE 315 n 92 ILE 315 B THR 316 n 93 THR 316 B VAL 317 n 94 VAL 317 B LYS 318 n 95 LYS 318 B author_and_software_defined_assembly PQS 4 tetrameric A MSE 237 SELENOMETHIONINE A MSE 14 MET A MSE 257 SELENOMETHIONINE A MSE 34 MET A MSE 278 SELENOMETHIONINE A MSE 55 MET B MSE 237 SELENOMETHIONINE B MSE 14 MET B MSE 257 SELENOMETHIONINE B MSE 34 MET B MSE 278 SELENOMETHIONINE B MSE 55 MET 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_556 y,x,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 68.4820000000 A N PHE 231 A N PHE 8 B O ASN 227 B O ASN 4 A O GLY 240 A O GLY 17 A N PHE 251 A N PHE 28 A N GLY 260 A N GLY 37 A O LEU 271 A O LEU 48 A O ALA 282 A O ALA 59 A N LEU 295 A N LEU 72 A N GLU 306 A N GLU 83 A O LYS 318 A O LYS 95 B O GLY 240 B O GLY 17 B N PHE 251 B N PHE 28 B N GLY 260 B N GLY 37 B O LEU 271 B O LEU 48 B O ALA 282 B O ALA 59 B N LEU 295 B N LEU 72 B N GLU 306 B N GLU 83 B O LYS 318 B O LYS 95 1 B CG ASP 225 B CG ASP 2 1 Y 1 B OD1 ASP 225 B OD1 ASP 2 1 Y 1 B OD2 ASP 225 B OD2 ASP 2 1 Y 1 B THR 224 B THR 1 1 Y 1 A LYS 265 53.13 76.00 1 A ASP 266 75.65 -21.79 1 B LYS 274 -80.38 -80.41 47.9 7.01 0.00 0.00 7.01 0.00 -14.02 SEVERAL CYCLES WITH CNS, ONE SHELX CYCLE TO FIND WATER MOLECULES, FINAL CYCLE WITH CNS 0.263 0.008 0.219 0.219 2.40 32.31 1046 12994 8.0 96.8 RANDOM 1544106.38 1 RESTRAINED THROUGHOUT 0.0 MAD FLAT MODEL 44.6129 0.344715 0.39 0.32 5.00 0.42 0.39 2.40 32.31 61 1655 42 0 1552 0.007 1.2 25.5 0.68 1.60 1.50 2.76 2.00 2.01 2.00 2.91 2.50 0.340 0.026 0.317 2.55 168 1953 6 7.9 97.0 46.3 2.400 30.000 1H8G 12997 8.000 0.04800 1 9.7000 3.000 97.8 2.40 2.53 1.600 0.36800 1 2.70 97.9 refinement CNS 1.0 data reduction MOSFLM data scaling SCALA phasing CNS MAJOR AUTOLYSIN (E.C.3.5.1.28) C-terminal domain of the major autolysin (C-LytA) from Streptococcus pneumoniae 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N THE CHOLINE-BINDING DOMAIN FRAGMENT CRYSTALLISES AS ATETRAMERIC ASSEMBLY FORMING A CYCLIC DOUGHNUT STRUCTURE. A ASP 303 A ASP 80 HELX_P A PRO 305 A PRO 82 5 1 3 B ASP 303 B ASP 80 HELX_P B PRO 305 B PRO 82 5 2 3 covale 1.327 both A GLU 236 A C GLU 13 1_555 A MSE 237 A N MSE 14 1_555 covale 1.330 both A MSE 237 A C MSE 14 1_555 A ALA 238 A N ALA 15 1_555 covale 1.330 both A ALA 256 A C ALA 33 1_555 A MSE 257 A N MSE 34 1_555 covale 1.332 both A MSE 257 A C MSE 34 1_555 A LYS 258 A N LYS 35 1_555 covale 1.326 both A ALA 277 A C ALA 54 1_555 A MSE 278 A N MSE 55 1_555 covale 1.329 both A MSE 278 A C MSE 55 1_555 A VAL 279 A N VAL 56 1_555 covale 1.331 both B GLU 236 B C GLU 13 1_555 B MSE 237 B N MSE 14 1_555 covale 1.325 both B MSE 237 B C MSE 14 1_555 B ALA 238 B N ALA 15 1_555 covale 1.331 both B ALA 256 B C ALA 33 1_555 B MSE 257 B N MSE 34 1_555 covale 1.330 both B MSE 257 B C MSE 34 1_555 B LYS 258 B N LYS 35 1_555 covale 1.326 both B ALA 277 B C ALA 54 1_555 B MSE 278 B N MSE 55 1_555 covale 1.329 both B MSE 278 B C MSE 55 1_555 B VAL 279 B N VAL 56 1_555 CHOLINE-BINDING DOMAIN CHOLINE-BINDING DOMAIN, CELL WALL ATTACHMENT given -0.755710 -0.197380 -0.624460 -0.252030 -0.792410 0.555480 -0.604470 0.577170 0.549080 154.17360 119.12921 17.23518 ALYS_STRPN UNP 1 P06653 224 318 1H8G 224 318 P06653 A 1 1 95 224 318 1H8G 224 318 P06653 B 1 1 95 1 MET modified residue MSE 237 1H8G A P06653 UNP 237 14 1 MET modified residue MSE 257 1H8G A P06653 UNP 257 34 1 MET modified residue MSE 278 1H8G A P06653 UNP 278 55 2 MET modified residue MSE 237 1H8G B P06653 UNP 237 14 2 MET modified residue MSE 257 1H8G B P06653 UNP 257 34 2 MET modified residue MSE 278 1H8G B P06653 UNP 278 55 2 2 2 2 2 2 2 2 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ASN 227 A ASN 4 A PHE 231 A PHE 8 B ASN 227 B ASN 4 B PHE 231 B PHE 8 A GLY 240 A GLY 17 A ILE 244 A ILE 21 A LYS 247 A LYS 24 A PHE 251 A PHE 28 A GLY 260 A GLY 37 A TYR 264 A TYR 41 A THR 267 A THR 44 A LEU 271 A LEU 48 A ALA 282 A ALA 59 A SER 286 A SER 63 A GLY 291 A GLY 68 A LEU 295 A LEU 72 A GLU 306 A GLU 83 A GLU 310 A GLU 87 A LEU 314 A LEU 91 A LYS 318 A LYS 95 B GLY 240 B GLY 17 B ILE 244 B ILE 21 B LYS 247 B LYS 24 B PHE 251 B PHE 28 B GLY 260 B GLY 37 B TYR 264 B TYR 41 B THR 267 B THR 44 B LEU 271 B LEU 48 B ALA 282 B ALA 59 B SER 286 B SER 63 B GLY 291 B GLY 68 B LEU 295 B LEU 72 B GLU 306 B GLU 83 B GLU 310 B GLU 87 B LEU 314 B LEU 91 B LYS 318 B LYS 95 BINDING SITE FOR RESIDUE CHT A 401 Software 2 BINDING SITE FOR RESIDUE CHT A 402 Software 3 BINDING SITE FOR RESIDUE CHT A 403 Software 1 BINDING SITE FOR RESIDUE CHT B 404 Software 5 BINDING SITE FOR RESIDUE CHT B 405 Software 3 BINDING SITE FOR RESIDUE CHT B 406 Software 1 A TRP 261 A TRP 38 2 1_555 A TYR 293 A TYR 70 2 1_555 A TRP 248 A TRP 25 3 1_555 A TYR 269 A TYR 46 3 1_555 A ASP 298 A ASP 75 3 1_555 A TYR 229 A TYR 6 1 1_555 A THR 224 A THR 1 5 1_555 A ASP 312 A ASP 89 5 1_555 B LYS 242 B LYS 19 5 1_555 B TRP 261 B TRP 38 5 1_555 B LEU 301 B LEU 78 5 1_555 A LYS 274 A LYS 51 3 1_555 A GLU 275 A GLU 52 3 1_555 B TYR 249 B TYR 26 3 1_555 B TYR 229 B TYR 6 1 1_555 92 P 41 21 2