HEADER TRANSFERASE/RNA 10-SEP-20 7D0F TITLE CRYO-EM STRUCTURE OF A PRE-CATALYTIC GROUP II INTRON RNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (738-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GROUP II INTRON-ENCODED PROTEIN LTRA; COMPND 7 CHAIN: C; COMPND 8 EC: 2.7.7.49,3.1.-.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 3 ORGANISM_TAXID: 1359; SOURCE 4 GENE: LTRB; SOURCE 5 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1359; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: IL1403; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 10 ORGANISM_TAXID: 1359; SOURCE 11 GENE: LTRA, MATR; SOURCE 12 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 1359; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: IL1403 KEYWDS CATALYTIC RNA, RNA-PROTEIN INTERACTIONS, GROUP II INTRON, KEYWDS 2 TRANSFERASE-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR N.LIU,X.L.DONG,C.X.HU,J.W.ZENG,J.W.WANG,J.WANG,H.W.WANG,M.BELFORT REVDAT 4 27-MAR-24 7D0F 1 REMARK REVDAT 3 18-NOV-20 7D0F 1 JRNL REVDAT 2 21-OCT-20 7D0F 1 JRNL REVDAT 1 30-SEP-20 7D0F 0 JRNL AUTH N.LIU,X.DONG,C.HU,J.ZENG,J.WANG,J.WANG,H.W.WANG,M.BELFORT JRNL TITL EXON AND PROTEIN POSITIONING IN A PRE-CATALYTIC GROUP II JRNL TITL 2 INTRON RNP PRIMED FOR SPLICING. JRNL REF NUCLEIC ACIDS RES. V. 48 11185 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 33021674 JRNL DOI 10.1093/NAR/GKAA773 REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5G2X REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 REMARK 3 NUMBER OF PARTICLES : 203373 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7D0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018490. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : A GROUP II INTRON --LTRB REMARK 245 COMPLEX WITH ITS REVERSE REMARK 245 TRANSCRIPTASE; GROUP II INTRON- REMARK 245 LTRB RNA; LTRA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 A A 415 REMARK 465 U A 416 REMARK 465 A A 417 REMARK 465 G A 418 REMARK 465 A A 419 REMARK 465 A A 2204 REMARK 465 U A 2205 REMARK 465 U A 2206 REMARK 465 C A 2207 REMARK 465 A A 2208 REMARK 465 C A 2209 REMARK 465 A A 2210 REMARK 465 A A 2211 REMARK 465 G A 2212 REMARK 465 A A 2213 REMARK 465 A A 2214 REMARK 465 A A 2215 REMARK 465 A A 2216 REMARK 465 U A 2217 REMARK 465 A A 2218 REMARK 465 U A 2219 REMARK 465 A A 2220 REMARK 465 G A 2221 REMARK 465 A A 2222 REMARK 465 C A 2223 REMARK 465 G A 2224 REMARK 465 A A 2225 REMARK 465 A A 2226 REMARK 465 G A 2227 REMARK 465 U A 2228 REMARK 465 U A 2229 REMARK 465 U A 2230 REMARK 465 U A 2231 REMARK 465 U A 2232 REMARK 465 A A 2233 REMARK 465 C A 2234 REMARK 465 A A 2235 REMARK 465 A A 2236 REMARK 465 G A 2237 REMARK 465 A A 2238 REMARK 465 C A 2239 REMARK 465 U A 2240 REMARK 465 U A 2241 REMARK 465 U A 2242 REMARK 465 A A 2243 REMARK 465 U A 2244 REMARK 465 C A 2245 REMARK 465 G A 2246 REMARK 465 U A 2247 REMARK 465 U A 2248 REMARK 465 A A 2249 REMARK 465 U A 2250 REMARK 465 C A 2251 REMARK 465 U A 2252 REMARK 465 U A 2253 REMARK 465 U A 2254 REMARK 465 U A 2255 REMARK 465 A A 2256 REMARK 465 C A 2257 REMARK 465 G A 2258 REMARK 465 U A 2259 REMARK 465 C A 2260 REMARK 465 C A 2261 REMARK 465 A A 2262 REMARK 465 G A 2263 REMARK 465 A A 2264 REMARK 465 U A 2265 REMARK 465 A A 2266 REMARK 465 U A 2267 REMARK 465 U A 2268 REMARK 465 U A 2269 REMARK 465 A A 2270 REMARK 465 U A 2271 REMARK 465 U A 2272 REMARK 465 A A 2273 REMARK 465 C A 2274 REMARK 465 G A 2275 REMARK 465 U A 2276 REMARK 465 G A 2277 REMARK 465 G A 2278 REMARK 465 C A 2279 REMARK 465 G A 2280 REMARK 465 A A 2281 REMARK 465 C A 2282 REMARK 465 G A 2283 REMARK 465 C A 2284 REMARK 465 G A 2285 REMARK 465 U A 2286 REMARK 465 U A 2287 REMARK 465 G A 2288 REMARK 465 G A 2289 REMARK 465 G A 2290 REMARK 465 A A 2291 REMARK 465 A A 2292 REMARK 465 A A 2293 REMARK 465 U A 2294 REMARK 465 G A 2295 REMARK 465 G A 2296 REMARK 465 C A 2297 REMARK 465 A A 2298 REMARK 465 A A 2299 REMARK 465 U A 2300 REMARK 465 G A 2301 REMARK 465 A A 2302 REMARK 465 U A 2303 REMARK 465 A A 2304 REMARK 465 G A 2305 REMARK 465 C A 2306 REMARK 465 G A 2307 REMARK 465 A A 2308 REMARK 465 A A 2309 REMARK 465 A A 2310 REMARK 465 C A 2311 REMARK 465 A A 2312 REMARK 465 A A 2313 REMARK 465 C A 2314 REMARK 465 G A 2315 REMARK 465 U A 2316 REMARK 465 A A 2317 REMARK 465 A A 2318 REMARK 465 A A 2319 REMARK 465 A A 2320 REMARK 465 C A 2321 REMARK 465 U A 2322 REMARK 465 C A 2323 REMARK 465 U A 2324 REMARK 465 U A 2325 REMARK 465 G A 2326 REMARK 465 U A 2327 REMARK 465 U A 2328 REMARK 465 G A 2329 REMARK 465 U A 2330 REMARK 465 A A 2331 REMARK 465 U A 2332 REMARK 465 G A 2333 REMARK 465 C A 2334 REMARK 465 U A 2335 REMARK 465 U A 2336 REMARK 465 U A 2337 REMARK 465 C A 2338 REMARK 465 A A 2339 REMARK 465 U A 2340 REMARK 465 U A 2341 REMARK 465 G A 2342 REMARK 465 U A 2343 REMARK 465 C A 2344 REMARK 465 A A 2345 REMARK 465 U A 2346 REMARK 465 C A 2347 REMARK 465 G A 2348 REMARK 465 U A 2349 REMARK 465 C A 2350 REMARK 465 A A 2351 REMARK 465 C A 2352 REMARK 465 G A 2353 REMARK 465 U A 2354 REMARK 465 G A 2355 REMARK 465 A A 2356 REMARK 465 U A 2357 REMARK 465 U A 2358 REMARK 465 C A 2359 REMARK 465 A A 2360 REMARK 465 U A 2361 REMARK 465 A A 2362 REMARK 465 A A 2363 REMARK 465 A A 2364 REMARK 465 C A 2365 REMARK 465 A A 2366 REMARK 465 C A 2367 REMARK 465 A A 2368 REMARK 465 A A 2369 REMARK 465 G A 2370 REMARK 465 U A 2371 REMARK 465 G A 2372 REMARK 465 A A 2373 REMARK 465 A A 2374 REMARK 465 U A 2375 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 PRO C 3 REMARK 465 TYR C 252 REMARK 465 ARG C 253 REMARK 465 GLU C 254 REMARK 465 LEU C 255 REMARK 465 HIS C 256 REMARK 465 ASN C 257 REMARK 465 GLU C 258 REMARK 465 ILE C 259 REMARK 465 LYS C 260 REMARK 465 ARG C 261 REMARK 465 ILE C 262 REMARK 465 SER C 263 REMARK 465 HIS C 264 REMARK 465 ARG C 265 REMARK 465 LEU C 266 REMARK 465 LYS C 267 REMARK 465 LYS C 268 REMARK 465 LEU C 269 REMARK 465 GLU C 270 REMARK 465 GLY C 271 REMARK 465 GLU C 272 REMARK 465 GLU C 273 REMARK 465 LYS C 274 REMARK 465 ALA C 275 REMARK 465 LYS C 276 REMARK 465 VAL C 277 REMARK 465 LEU C 278 REMARK 465 LEU C 279 REMARK 465 GLU C 280 REMARK 465 TYR C 281 REMARK 465 GLN C 282 REMARK 465 GLU C 283 REMARK 465 LYS C 284 REMARK 465 ARG C 285 REMARK 465 LYS C 286 REMARK 465 ARG C 287 REMARK 465 LEU C 288 REMARK 465 PRO C 289 REMARK 465 THR C 290 REMARK 465 LEU C 291 REMARK 465 PRO C 292 REMARK 465 CYS C 293 REMARK 465 THR C 294 REMARK 465 SER C 295 REMARK 465 GLN C 296 REMARK 465 THR C 297 REMARK 465 ASN C 298 REMARK 465 LYS C 299 REMARK 465 VAL C 300 REMARK 465 LEU C 301 REMARK 465 ARG C 364 REMARK 465 ARG C 365 REMARK 465 SER C 366 REMARK 465 GLY C 367 REMARK 465 THR C 368 REMARK 465 ILE C 369 REMARK 465 LYS C 370 REMARK 465 ARG C 371 REMARK 465 SER C 372 REMARK 465 GLY C 373 REMARK 465 LYS C 374 REMARK 465 ILE C 491 REMARK 465 PRO C 492 REMARK 465 TYR C 493 REMARK 465 GLU C 494 REMARK 465 ILE C 495 REMARK 465 LYS C 496 REMARK 465 GLN C 497 REMARK 465 GLY C 498 REMARK 465 LYS C 499 REMARK 465 GLN C 500 REMARK 465 ARG C 501 REMARK 465 ARG C 502 REMARK 465 TYR C 503 REMARK 465 PHE C 504 REMARK 465 ALA C 505 REMARK 465 ASN C 506 REMARK 465 PHE C 507 REMARK 465 SER C 508 REMARK 465 GLU C 509 REMARK 465 CYS C 510 REMARK 465 LYS C 511 REMARK 465 SER C 512 REMARK 465 PRO C 513 REMARK 465 TYR C 514 REMARK 465 GLN C 515 REMARK 465 PHE C 516 REMARK 465 THR C 517 REMARK 465 ASP C 518 REMARK 465 GLU C 519 REMARK 465 LYS C 541 REMARK 465 CYS C 542 REMARK 465 CYS C 543 REMARK 465 GLU C 544 REMARK 465 LEU C 545 REMARK 465 CYS C 546 REMARK 465 GLY C 547 REMARK 465 THR C 548 REMARK 465 SER C 549 REMARK 465 ASP C 550 REMARK 465 GLU C 551 REMARK 465 ASN C 552 REMARK 465 THR C 553 REMARK 465 SER C 554 REMARK 465 TYR C 555 REMARK 465 GLU C 556 REMARK 465 ILE C 557 REMARK 465 HIS C 558 REMARK 465 HIS C 559 REMARK 465 VAL C 560 REMARK 465 ASN C 561 REMARK 465 LYS C 562 REMARK 465 VAL C 563 REMARK 465 LYS C 564 REMARK 465 ASN C 565 REMARK 465 LEU C 566 REMARK 465 LYS C 567 REMARK 465 GLY C 568 REMARK 465 LYS C 569 REMARK 465 GLU C 570 REMARK 465 LYS C 571 REMARK 465 TRP C 572 REMARK 465 GLU C 573 REMARK 465 MET C 574 REMARK 465 ALA C 575 REMARK 465 MET C 576 REMARK 465 ILE C 577 REMARK 465 ALA C 578 REMARK 465 LYS C 579 REMARK 465 GLN C 580 REMARK 465 ARG C 581 REMARK 465 LYS C 582 REMARK 465 THR C 583 REMARK 465 LEU C 584 REMARK 465 VAL C 585 REMARK 465 VAL C 586 REMARK 465 CYS C 587 REMARK 465 PHE C 588 REMARK 465 HIS C 589 REMARK 465 CYS C 590 REMARK 465 HIS C 591 REMARK 465 ARG C 592 REMARK 465 HIS C 593 REMARK 465 VAL C 594 REMARK 465 ILE C 595 REMARK 465 HIS C 596 REMARK 465 LYS C 597 REMARK 465 HIS C 598 REMARK 465 LYS C 599 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N2 G A 2439 O4' C A 2484 1.79 REMARK 500 N6 A A -8 O4 U A 222 1.96 REMARK 500 N1 G A 561 O2 C A 568 1.97 REMARK 500 N6 A A 484 O2' A A 516 1.98 REMARK 500 N7 A A 248 N4 C A 251 1.99 REMARK 500 O2 U A 477 N2 G A 520 2.01 REMARK 500 N1 G A 2436 O4 U A 2487 2.01 REMARK 500 O2 U A 182 O6 G A 352 2.02 REMARK 500 O MET C 459 OG SER C 462 2.02 REMARK 500 O ALA C 142 NZ LYS C 147 2.02 REMARK 500 N1 A A 58 C6 G A 294 2.02 REMARK 500 O CYS C 463 OG1 THR C 466 2.02 REMARK 500 O2' G A 491 O2' G A 513 2.03 REMARK 500 O2 C A 354 N2 G A 2413 2.03 REMARK 500 O2' A A 336 OP2 G A 338 2.03 REMARK 500 O2' A A 585 O4 U A 587 2.04 REMARK 500 O ILE C 11 OG SER C 15 2.04 REMARK 500 O6 G A 234 O2 U A 255 2.04 REMARK 500 OD1 ASP C 241 OG SER C 244 2.05 REMARK 500 N1 A A 58 O6 G A 294 2.05 REMARK 500 N6 A A 53 O2 C A 299 2.05 REMARK 500 O6 G A 432 O4 U A 449 2.05 REMARK 500 N LEU C 55 O THR C 58 2.06 REMARK 500 O2 U A 212 O6 G A 338 2.06 REMARK 500 O2' A A 2398 OP1 C A 2492 2.06 REMARK 500 O2' U A 317 N1 G A 332 2.06 REMARK 500 O2 U A 2408 N2 G A 2417 2.07 REMARK 500 N2 G A 561 O2 C A 568 2.08 REMARK 500 O2' A A 186 N2 G A 2399 2.08 REMARK 500 O GLU C 427 OG1 THR C 430 2.09 REMARK 500 O2' G A 106 OP1 A A 110 2.09 REMARK 500 N1 A A 2447 O6 G A 2475 2.09 REMARK 500 O2' A A 40 O2 U A 368 2.09 REMARK 500 O GLY C 215 OG SER C 218 2.09 REMARK 500 N1 A A 481 O2' A A 515 2.10 REMARK 500 C2 G A 561 O2 C A 568 2.10 REMARK 500 O2' A A 546 OP2 A A 585 2.10 REMARK 500 OD1 ASP C 128 NH2 ARG C 305 2.10 REMARK 500 N6 A A 400 O2' C A 461 2.10 REMARK 500 O2 U A 551 N6 A A 586 2.10 REMARK 500 O ILE C 117 OG SER C 120 2.11 REMARK 500 N1 G A 318 N7 A A 335 2.11 REMARK 500 O2 U A -3 O6 G A 282 2.11 REMARK 500 O2 U A 497 N4 C A 502 2.11 REMARK 500 O2' G A 5 OP2 G A 470 2.11 REMARK 500 O2' G A 5 N6 A A 2420 2.11 REMARK 500 OG SER C 486 O ALA C 523 2.11 REMARK 500 O2' G A 37 O2 C A 371 2.12 REMARK 500 N3 U A 198 O2' A A 200 2.12 REMARK 500 O6 G A 190 O2' G A 343 2.13 REMARK 500 REMARK 500 THIS ENTRY HAS 98 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 A A 523 N9 A A 523 C4 -0.042 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 C A 7 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 C A 111 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 G A 121 N3 - C4 - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 C A 122 N1 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 C A 122 C6 - N1 - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 C A 122 C2 - N1 - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 G A 123 N3 - C4 - C5 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 123 N3 - C4 - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 G A 123 C8 - N9 - C1' ANGL. DEV. = 7.8 DEGREES REMARK 500 G A 123 C4 - N9 - C1' ANGL. DEV. = -8.8 DEGREES REMARK 500 A A 137 C6 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 G A 138 C4 - C5 - N7 ANGL. DEV. = 2.4 DEGREES REMARK 500 A A 156 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 G A 160 N3 - C4 - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 G A 199 C6 - C5 - N7 ANGL. DEV. = 4.2 DEGREES REMARK 500 G A 199 N1 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 G A 199 C8 - N9 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 G A 199 C4 - N9 - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 A A 201 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A 211 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 211 C6 - N1 - C1' ANGL. DEV. = 8.8 DEGREES REMARK 500 C A 211 C2 - N1 - C1' ANGL. DEV. = -8.8 DEGREES REMARK 500 U A 224 C6 - N1 - C1' ANGL. DEV. = -9.4 DEGREES REMARK 500 U A 224 C2 - N1 - C1' ANGL. DEV. = 10.0 DEGREES REMARK 500 G A 225 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 U A 226 C5 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 233 N1 - C2 - N3 ANGL. DEV. = 3.5 DEGREES REMARK 500 G A 234 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 316 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 C A 316 C2 - N1 - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 A A 339 N1 - C2 - N3 ANGL. DEV. = 3.2 DEGREES REMARK 500 C A 342 C2 - N1 - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 G A 465 N3 - C4 - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 502 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 C A 502 C6 - N1 - C1' ANGL. DEV. = -8.3 DEGREES REMARK 500 C A 502 C2 - N1 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 C A 514 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 514 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 523 N1 - C2 - N3 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 523 C2 - N3 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 U A 533 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES REMARK 500 U A 544 C2 - N1 - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 C A 584 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A2382 C8 - N9 - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 G A2382 C4 - N9 - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 A A2383 C6 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 A A2383 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A2397 N3 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 G A2397 N3 - C4 - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 54 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER C 15 57.76 36.48 REMARK 500 ASP C 20 124.93 -37.15 REMARK 500 GLU C 21 -146.37 -154.82 REMARK 500 VAL C 22 130.78 -35.10 REMARK 500 GLN C 41 -33.32 -130.06 REMARK 500 LYS C 52 50.58 -96.37 REMARK 500 ASP C 56 -13.67 70.03 REMARK 500 ASP C 57 -19.91 -142.66 REMARK 500 GLU C 65 73.03 59.28 REMARK 500 ILE C 67 -64.32 -103.53 REMARK 500 LYS C 68 -63.38 -95.56 REMARK 500 GLN C 82 78.28 42.55 REMARK 500 SER C 94 70.60 48.86 REMARK 500 LYS C 96 107.31 -161.07 REMARK 500 ILE C 102 107.63 -57.03 REMARK 500 PRO C 124 44.29 -95.46 REMARK 500 VAL C 125 -54.96 -131.93 REMARK 500 ASP C 128 80.64 60.11 REMARK 500 VAL C 129 164.07 -47.35 REMARK 500 SER C 130 168.02 -43.29 REMARK 500 HIS C 131 131.42 -31.42 REMARK 500 ARG C 154 -165.91 -75.49 REMARK 500 TRP C 155 69.96 71.61 REMARK 500 LYS C 162 -65.24 -93.57 REMARK 500 HIS C 170 -6.82 66.51 REMARK 500 ALA C 196 23.34 -76.02 REMARK 500 ASN C 201 44.83 -144.32 REMARK 500 TRP C 202 -4.58 71.41 REMARK 500 TYR C 208 -38.21 -132.63 REMARK 500 PHE C 240 -66.76 -93.99 REMARK 500 ASP C 241 50.76 -91.09 REMARK 500 PRO C 245 42.97 -84.48 REMARK 500 GLU C 246 -23.33 -140.06 REMARK 500 SER C 313 -157.96 -78.66 REMARK 500 SER C 317 -169.63 -102.94 REMARK 500 LYS C 337 -1.51 81.48 REMARK 500 GLU C 342 25.20 49.31 REMARK 500 GLU C 343 72.55 57.99 REMARK 500 LYS C 344 -56.43 -26.16 REMARK 500 THR C 345 -4.15 -140.96 REMARK 500 ILE C 347 131.73 -39.02 REMARK 500 SER C 350 -169.18 -79.78 REMARK 500 ALA C 354 -169.48 -114.56 REMARK 500 PHE C 356 84.67 -151.82 REMARK 500 LEU C 357 16.72 53.32 REMARK 500 LYS C 376 52.94 -91.57 REMARK 500 LYS C 407 110.98 -162.92 REMARK 500 HIS C 416 -83.23 -61.07 REMARK 500 ARG C 417 78.51 -167.07 REMARK 500 LYS C 418 27.01 38.03 REMARK 500 REMARK 500 THIS ENTRY HAS 55 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR C 44 SER C 45 149.36 REMARK 500 LYS C 69 ILE C 70 145.00 REMARK 500 TYR C 122 GLU C 123 -146.48 REMARK 500 VAL C 129 SER C 130 -137.40 REMARK 500 SER C 130 HIS C 131 -141.31 REMARK 500 ALA C 153 ARG C 154 -147.84 REMARK 500 ASP C 160 ILE C 161 -148.85 REMARK 500 GLU C 343 LYS C 344 -130.67 REMARK 500 LYS C 407 LYS C 408 146.60 REMARK 500 HIS C 416 ARG C 417 137.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30532 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A PRE-CATALYTIC GROUP II INTRON RNP DBREF 7D0F A -11 2493 PDB 7D0F 7D0F -11 2493 DBREF 7D0F C 1 599 UNP P0A3U0 LTRA_LACLC 1 599 SEQRES 1 A 915 C A C A U C C A U A A C G SEQRES 2 A 915 U G C G C C C A G A U A G SEQRES 3 A 915 G G U G U U A A G U C A A SEQRES 4 A 915 G U A G U U U A A G G U A SEQRES 5 A 915 C U A C U C U G U A A G A SEQRES 6 A 915 U A A C A C A G A A A A C SEQRES 7 A 915 A G C C A A C C U A A C C SEQRES 8 A 915 G A A A A G C G A A A G C SEQRES 9 A 915 U G A U A C G G G A A C A SEQRES 10 A 915 G A G C A C G G U U G G A SEQRES 11 A 915 A A G C G A U G A G U U A SEQRES 12 A 915 C C U A A A G A C A A U C SEQRES 13 A 915 G G G U A C G A C U G A G SEQRES 14 A 915 U C G C A A U G U U A A U SEQRES 15 A 915 C A G A U A U A A G G U A SEQRES 16 A 915 U A A G U U G U G U U U A SEQRES 17 A 915 C U G A A C G C A A G U U SEQRES 18 A 915 U C U A A U U U C G G U U SEQRES 19 A 915 A U G U G U C G A U A G A SEQRES 20 A 915 G G A A A G U G U C U G A SEQRES 21 A 915 A A C C U C U A G U A C A SEQRES 22 A 915 A A G A A A G G U A A G U SEQRES 23 A 915 U A U G G U U G U G G A C SEQRES 24 A 915 U U A U C U G U U A U C A SEQRES 25 A 915 C C A C A U U U G U A C A SEQRES 26 A 915 A U C U G U A G G A G A A SEQRES 27 A 915 C C U A U G G G A A C G A SEQRES 28 A 915 A A C G A A A G C G A U G SEQRES 29 A 915 C C G A G A A U C U G A A SEQRES 30 A 915 U U U A C C A A G A C U U SEQRES 31 A 915 A A C A C U A A C U G G G SEQRES 32 A 915 G A U A C C C U A A A C A SEQRES 33 A 915 A G A A U G C C U A A U A SEQRES 34 A 915 G A A A G G A G G A A A A SEQRES 35 A 915 A G G C U A U A G C A C U SEQRES 36 A 915 A G A G C U U G A A A A U SEQRES 37 A 915 C U U G C A A G G G U A C SEQRES 38 A 915 G G A G U A C U C G U A G SEQRES 39 A 915 U A G U C U G A G A A G G SEQRES 40 A 915 G U A A C G C C C U U U A SEQRES 41 A 915 C A U G G C A A A G G G G SEQRES 42 A 915 U A C A G U U A U U G U G SEQRES 43 A 915 U A C U A A A A U U A A A SEQRES 44 A 915 A A U U G A U U A G G G A SEQRES 45 A 915 G G A A A A C C U C A A A SEQRES 46 A 915 A U G A A A C C A A C A A SEQRES 47 A 915 U G G C A A U U U U A G A SEQRES 48 A 915 A A G A A U C A G U A A A SEQRES 49 A 915 A A U U C A C A A G A A A SEQRES 50 A 915 A U A U A G A C G A A G U SEQRES 51 A 915 U U U U A C A A G A C U U SEQRES 52 A 915 U A U C G U U A U C U U U SEQRES 53 A 915 U A C G U C C A G A U A U SEQRES 54 A 915 U U A U U A C G U G G C G SEQRES 55 A 915 A C G C G U U G G G A A A SEQRES 56 A 915 U G G C A A U G A U A G C SEQRES 57 A 915 G A A A C A A C G U A A A SEQRES 58 A 915 A C U C U U G U U G U A U SEQRES 59 A 915 G C U U U C A U U G U C A SEQRES 60 A 915 U C G U C A C G U G A U U SEQRES 61 A 915 C A U A A A C A C A A G U SEQRES 62 A 915 G A A U U U U U A C G A A SEQRES 63 A 915 C G A A C A A U A A C A G SEQRES 64 A 915 A G C C G U A U A C U C C SEQRES 65 A 915 G A G A G G G G U A C G U SEQRES 66 A 915 A C G G U U C C C G A A G SEQRES 67 A 915 A G G G U G G U G C A A A SEQRES 68 A 915 C C A G U C A C A G U A A SEQRES 69 A 915 U G U G A A C A A G G C G SEQRES 70 A 915 G U A C C U C C C U C U U SEQRES 71 A 915 C A C C A SEQRES 1 C 599 MET LYS PRO THR MET ALA ILE LEU GLU ARG ILE SER LYS SEQRES 2 C 599 ASN SER GLN GLU ASN ILE ASP GLU VAL PHE THR ARG LEU SEQRES 3 C 599 TYR ARG TYR LEU LEU ARG PRO ASP ILE TYR TYR VAL ALA SEQRES 4 C 599 TYR GLN ASN LEU TYR SER ASN LYS GLY ALA SER THR LYS SEQRES 5 C 599 GLY ILE LEU ASP ASP THR ALA ASP GLY PHE SER GLU GLU SEQRES 6 C 599 LYS ILE LYS LYS ILE ILE GLN SER LEU LYS ASP GLY THR SEQRES 7 C 599 TYR TYR PRO GLN PRO VAL ARG ARG MET TYR ILE ALA LYS SEQRES 8 C 599 LYS ASN SER LYS LYS MET ARG PRO LEU GLY ILE PRO THR SEQRES 9 C 599 PHE THR ASP LYS LEU ILE GLN GLU ALA VAL ARG ILE ILE SEQRES 10 C 599 LEU GLU SER ILE TYR GLU PRO VAL PHE GLU ASP VAL SER SEQRES 11 C 599 HIS GLY PHE ARG PRO GLN ARG SER CYS HIS THR ALA LEU SEQRES 12 C 599 LYS THR ILE LYS ARG GLU PHE GLY GLY ALA ARG TRP PHE SEQRES 13 C 599 VAL GLU GLY ASP ILE LYS GLY CYS PHE ASP ASN ILE ASP SEQRES 14 C 599 HIS VAL THR LEU ILE GLY LEU ILE ASN LEU LYS ILE LYS SEQRES 15 C 599 ASP MET LYS MET SER GLN LEU ILE TYR LYS PHE LEU LYS SEQRES 16 C 599 ALA GLY TYR LEU GLU ASN TRP GLN TYR HIS LYS THR TYR SEQRES 17 C 599 SER GLY THR PRO GLN GLY GLY ILE LEU SER PRO LEU LEU SEQRES 18 C 599 ALA ASN ILE TYR LEU HIS GLU LEU ASP LYS PHE VAL LEU SEQRES 19 C 599 GLN LEU LYS MET LYS PHE ASP ARG GLU SER PRO GLU ARG SEQRES 20 C 599 ILE THR PRO GLU TYR ARG GLU LEU HIS ASN GLU ILE LYS SEQRES 21 C 599 ARG ILE SER HIS ARG LEU LYS LYS LEU GLU GLY GLU GLU SEQRES 22 C 599 LYS ALA LYS VAL LEU LEU GLU TYR GLN GLU LYS ARG LYS SEQRES 23 C 599 ARG LEU PRO THR LEU PRO CYS THR SER GLN THR ASN LYS SEQRES 24 C 599 VAL LEU LYS TYR VAL ARG TYR ALA ASP ASP PHE ILE ILE SEQRES 25 C 599 SER VAL LYS GLY SER LYS GLU ASP CYS GLN TRP ILE LYS SEQRES 26 C 599 GLU GLN LEU LYS LEU PHE ILE HIS ASN LYS LEU LYS MET SEQRES 27 C 599 GLU LEU SER GLU GLU LYS THR LEU ILE THR HIS SER SER SEQRES 28 C 599 GLN PRO ALA ARG PHE LEU GLY TYR ASP ILE ARG VAL ARG SEQRES 29 C 599 ARG SER GLY THR ILE LYS ARG SER GLY LYS VAL LYS LYS SEQRES 30 C 599 ARG THR LEU ASN GLY SER VAL GLU LEU LEU ILE PRO LEU SEQRES 31 C 599 GLN ASP LYS ILE ARG GLN PHE ILE PHE ASP LYS LYS ILE SEQRES 32 C 599 ALA ILE GLN LYS LYS ASP SER SER TRP PHE PRO VAL HIS SEQRES 33 C 599 ARG LYS TYR LEU ILE ARG SER THR ASP LEU GLU ILE ILE SEQRES 34 C 599 THR ILE TYR ASN SER GLU LEU ARG GLY ILE CYS ASN TYR SEQRES 35 C 599 TYR GLY LEU ALA SER ASN PHE ASN GLN LEU ASN TYR PHE SEQRES 36 C 599 ALA TYR LEU MET GLU TYR SER CYS LEU LYS THR ILE ALA SEQRES 37 C 599 SER LYS HIS LYS GLY THR LEU SER LYS THR ILE SER MET SEQRES 38 C 599 PHE LYS ASP GLY SER GLY SER TRP GLY ILE PRO TYR GLU SEQRES 39 C 599 ILE LYS GLN GLY LYS GLN ARG ARG TYR PHE ALA ASN PHE SEQRES 40 C 599 SER GLU CYS LYS SER PRO TYR GLN PHE THR ASP GLU ILE SEQRES 41 C 599 SER GLN ALA PRO VAL LEU TYR GLY TYR ALA ARG ASN THR SEQRES 42 C 599 LEU GLU ASN ARG LEU LYS ALA LYS CYS CYS GLU LEU CYS SEQRES 43 C 599 GLY THR SER ASP GLU ASN THR SER TYR GLU ILE HIS HIS SEQRES 44 C 599 VAL ASN LYS VAL LYS ASN LEU LYS GLY LYS GLU LYS TRP SEQRES 45 C 599 GLU MET ALA MET ILE ALA LYS GLN ARG LYS THR LEU VAL SEQRES 46 C 599 VAL CYS PHE HIS CYS HIS ARG HIS VAL ILE HIS LYS HIS SEQRES 47 C 599 LYS HELIX 1 AA1 ILE C 7 ASN C 14 1 8 HELIX 2 AA2 LEU C 30 GLN C 41 1 12 HELIX 3 AA3 THR C 104 ILE C 121 1 18 HELIX 4 AA4 SER C 138 ILE C 146 1 9 HELIX 5 AA5 HIS C 170 LYS C 182 1 13 HELIX 6 AA6 LEU C 217 ASP C 241 1 25 HELIX 7 AA7 LYS C 318 LEU C 336 1 19 HELIX 8 AA8 LEU C 390 LYS C 402 1 13 HELIX 9 AA9 THR C 424 TYR C 443 1 20 HELIX 10 AB1 ASN C 448 LYS C 470 1 23 HELIX 11 AB2 SER C 476 ASP C 484 1 9 HELIX 12 AB3 LEU C 526 ASN C 536 1 11 SHEET 1 AA1 2 VAL C 84 ARG C 85 0 SHEET 2 AA1 2 LEU C 199 GLU C 200 1 O GLU C 200 N VAL C 84 SHEET 1 AA2 2 TYR C 88 ALA C 90 0 SHEET 2 AA2 2 MET C 97 PRO C 99 -1 O ARG C 98 N ILE C 89 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000