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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF E. COLI RNASE E POSSESSING M1 RNA FRAGMENTS - CATALYTIC DOMAIN
Keywords RNA PROCESSING, M1 RNA, RNASE P, NUCLEASE, HYDROLASE, CYTOPLASM, RNA-BINDING, RNA TURNOVER, ENDONUCLEASE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2VRT     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   RIBONUCLEASE E  A 468 3465 0
2  Protein   RIBONUCLEASE E  B 398 2915 0
3  Protein   RIBONUCLEASE E  C 411 2966 0
4  Protein   RIBONUCLEASE E  D 487 3628 0
5  RNA    E 2 41 0
6  RNA    F 2 41 0
7  RNA    G 3 64 0
8  RNA    H 3 64 0
9  Ligand   RIBONUCLEASE E  A 1 0 1
10  Ligand   RIBONUCLEASE E  D 1 0 1
total       1776 13184 2
Proteins
Unit 1 MET1 LYS2 ARG3 MET4 LEU5 ILE6 ASN7 ALA8 THR9 GLN10 GLN11 GLU12 GLU13 LEU14 ARG15 VAL16 ALA17 LEU18 VAL19 ASP20 GLY21 GLN22 ARG23 LEU24 TYR25 ASP26 LEU27 ASP28 ILE29 GLU30 SER31 PRO32 GLU35 GLN36 LYS37 LYS38 ALA39 ASN40 ILE41 TYR42 LYS43 GLY44 LYS45 ILE46 THR47 ARG48 ILE49 GLU50 PRO51 SER52 LEU53 GLU54 ALA55 ALA56 PHE57 VAL58 ASP59 TYR60 GLY61 ALA62 GLU63 ARG64 HIS65 GLY66 PHE67 LEU68 PRO69 LEU70 LYS71 GLU72 ILE73 ALA74 ARG75 GLU76 TYR77 PHE78 PRO79 ARG87 PRO88 ASN89 ILE90 LYS91 ASP92 VAL93 LEU94 ARG95 GLU96 GLY97 GLN98 GLU99 VAL100 ILE101 VAL102 GLN103 ILE104 ASP105 LYS106 GLU107 GLU108 ARG109 GLY110 ASN111 LYS112 GLY113 ALA114 ALA115 LEU116 THR117 THR118 PHE119 ILE120 SER121 LEU122 ALA123 GLY124 SER125 TYR126 LEU127 VAL128 LEU129 MET130 PRO131 ASN132 ASN133 PRO134 ARG135 ALA136 GLY137 GLY138 ILE139 SER140 ARG141 ARG142 ILE143 GLU144 GLY145 ASP146 ASP147 ARG148 THR149 GLU150 LEU151 LYS152 GLU153 ALA154 LEU155 ALA156 SER157 LEU158 GLU159 LEU160 PRO161 GLU162 GLY163 MET164 GLY165 LEU166 ILE167 VAL168 ARG169 THR170 ALA171 GLY172 VAL173 GLY174 LYS175 SER176 ALA177 GLU178 ALA179 LEU180 GLN181 TRP182 ASP183 LEU184 SER185 PHE186 ARG187 LEU188 LYS189 HIS190 TRP191 GLU192 ALA193 ILE194 LYS195 LYS196 ALA197 ALA198 GLU199 SER200 ARG201 PRO202 ALA203 PRO204 PHE205 LEU206 ILE207 HIS208 GLN209 GLU210 SER211 ASN212 VAL213 ILE214 VAL215 ARG216 ALA217 PHE218 ARG219 ASP220 TYR221 LEU222 ARG223 GLN224 ASP225 ILE226 GLY227 GLU228 ILE229 LEU230 ILE231 ASP232 ASN233 PRO234 LYS235 VAL236 LEU237 GLU238 LEU239 ALA240 ARG241 GLN242 HIS243 ILE244 ALA245 ALA246 LEU247 GLY248 ARG249 PRO250 ASP251 PHE252 SER253 SER254 LYS255 ILE256 LYS257 LEU258 TYR259 THR260 GLY261 GLU262 ILE263 PRO264 LEU265 PHE266 SER267 HIS268 TYR269 GLN270 ILE271 GLU272 SER273 GLN274 ILE275 GLU276 SER277 ALA278 PHE279 GLN280 ARG281 GLU282 VAL283 ARG284 LEU285 PRO286 SER287 GLY288 GLY289 SER290 ILE291 VAL292 ILE293 ASP294 SER295 THR296 GLU297 ALA298 LEU299 THR300 ALA301 ILE302 ASP303 ILE304 ASN305 SER306 ALA307 ARG308 ASP314 ILE315 GLU316 GLU317 THR318 ALA319 PHE320 ASN321 THR322 ASN323 LEU324 GLU325 ALA326 ALA327 ASP328 GLU329 ILE330 ALA331 ARG332 GLN333 LEU334 ARG335 LEU336 ARG337 ASP338 LEU339 GLY340 GLY341 LEU342 ILE343 VAL344 ILE345 ASP346 PHE347 ILE348 ASP349 MET350 THR351 PRO352 VAL353 ARG354 HIS355 GLN356 ARG357 ALA358 VAL359 GLU360 ASN361 ARG362 LEU363 ARG364 GLU365 ALA366 VAL367 ARG368 GLN369 ASP370 ARG371 ALA372 ARG373 ILE374 GLN375 ILE376 SER377 HIS378 ILE379 SER380 ARG381 PHE382 GLY383 LEU384 LEU385 GLU386 MET387 SER388 ARG389 GLN390 ARG391 LEU392 SER393 HIS402 VAL403 CYS404 CYS407 THR412 VAL413 ARG414 ASP415 ASN416 GLU417 SER418 LEU419 SER420 LEU421 SER422 ILE423 LEU424 ARG425 LEU426 ILE427 GLU428 GLU429 GLU430 ALA431 LEU432 LYS433 GLU434 ASN435 THR436 ALA441 ILE442 VAL443 PRO444 VAL445 PRO446 ILE447 ALA448 SER449 TYR450 LEU451 LEU452 ASN453 GLU454 LYS455 ARG456 SER457 ALA458 VAL459 ASN460 ALA461 ILE462 GLU463 THR464 ARG465 GLN466 ASP467 GLY468 VAL469 ARG470 CYS471 VAL472 ILE473 VAL474 PRO475 ASN476 ASP477 GLN478 MET479 GLU480 THR481 PRO482 HIS483 TYR484 HIS485 VAL486 LEU487 ARG488 VAL489 THR495 PRO496 THR497 LEU498 SER499 TYR500 MET501 LEU502 PRO503 LYS504 LEU505
Unit 2 MET1 LYS2 ARG3 MET4 LEU5 ILE6 ASN7 ALA8 THR9 GLN10 GLN11 GLU12 GLU13 LEU14 ARG15 VAL16 ALA17 LEU18 VAL19 ASP20 GLY21 GLN22 ARG23 LEU24 TYR25 ASP26 LEU27 ASP28 ILE29 PHE119 ILE120 SER121 LEU122 ALA123 GLY124 SER125 TYR126 LEU127 VAL128 LEU129 MET130 PRO131 ASN132 ASN133 PRO134 ARG135 ALA136 GLY137 GLY138 ILE139 SER140 ARG141 ARG142 ILE143 GLU144 GLY145 ASP146 ASP147 ARG148 THR149 GLU150 LEU151 LYS152 GLU153 ALA154 LEU155 ALA156 SER157 LEU158 GLU159 LEU160 PRO161 GLU162 GLY163 MET164 GLY165 LEU166 ILE167 VAL168 ARG169 THR170 ALA171 GLY172 VAL173 SER176 ALA177 GLU178 ALA179 LEU180 GLN181 TRP182 ASP183 LEU184 SER185 PHE186 ARG187 LEU188 LYS189 HIS190 TRP191 GLU192 ALA193 ILE194 LYS195 LYS196 ALA197 ALA198 GLU199 SER200 ALA203 PRO204 PHE205 LEU206 ILE207 HIS208 GLN209 ASN212 VAL213 ILE214 VAL215 ARG216 ALA217 PHE218 ARG219 ASP220 TYR221 LEU222 ARG223 ASP225 ILE226 GLY227 GLU228 ILE229 LEU230 ILE231 ASP232 ASN233 PRO234 LYS235 VAL236 LEU237 GLU238 LEU239 ALA240 ARG241 GLN242 HIS243 ILE244 ALA245 PRO250 ASP251 PHE252 SER253 SER254 LYS255 ILE256 LYS257 LEU258 TYR259 THR260 GLY261 GLU262 ILE263 PRO264 LEU265 PHE266 SER267 HIS268 TYR269 GLN270 ILE271 GLU272 SER273 GLN274 ILE275 GLU276 SER277 ALA278 PHE279 GLN280 ARG281 GLU282 VAL283 ARG284 LEU285 PRO286 SER287 GLY288 GLY289 SER290 ILE291 VAL292 ILE293 ASP294 SER295 THR296 GLU297 ALA298 LEU299 THR300 ALA301 ILE302 ASP303 ILE304 ASN305 SER306 ALA307 GLY313 ASP314 ILE315 GLU316 GLU317 THR318 ALA319 PHE320 ASN321 THR322 ASN323 LEU324 GLU325 ALA326 ALA327 ASP328 GLU329 ILE330 ALA331 ARG332 GLN333 LEU334 ARG335 LEU336 ARG337 ASP338 LEU339 GLY340 GLY341 LEU342 ILE343 VAL344 ILE345 ASP346 PHE347 ILE348 ASP349 MET350 THR351 PRO352 VAL353 ARG354 HIS355 GLN356 ARG357 ALA358 VAL359 GLU360 ASN361 ARG362 LEU363 ARG364 GLU365 ALA366 VAL367 ARG368 GLN369 ASP370 ARG371 ALA372 ARG373 ILE374 GLN375 ILE376 SER377 HIS378 ILE379 SER380 ARG381 PHE382 GLY383 LEU384 LEU385 GLU386 MET387 SER388 ARG389 GLN390 ARG391 LEU392 SER393 PRO394 SER395 HIS401 HIS402 VAL403 CYS404 PRO405 ARG406 CYS407 SER408 GLY409 THR410 GLY411 THR412 VAL413 ARG414 ASP415 ASN416 GLU417 SER418 LEU419 SER420 LEU421 SER422 ILE423 LEU424 ARG425 LEU426 ILE427 GLU428 GLU429 GLU430 ALA431 LEU432 LYS433 GLU434 ASN435 THR436 GLN437 GLU438 VAL439 HIS440 ALA441 ILE442 VAL443 PRO444 VAL445 PRO446 ILE447 ALA448 SER449 TYR450 LEU451 LEU452 ASN453 GLU454 LYS455 ARG456 SER457 ALA458 VAL459 ASN460 ALA461 ILE462 GLU463 THR464 ARG465 GLN466 ASP467 GLY468 VAL469 ARG470 CYS471 VAL472 ILE473 VAL474 PRO475 ASN476 ASP477 GLN478 MET479 GLU480 THR481 PRO482 HIS483 TYR484 HIS485 VAL486 LEU487 ARG488 VAL489 ARG490 LYS491 GLY492 GLU493 GLU494 THR495 PRO496 THR497 LEU498 SER499 TYR500 MET501 LEU502 PRO503 LYS504 LEU505 HIS506 GLU507 GLU508
Unit 3 MET1 LYS2 ARG3 MET4 LEU5 ILE6 ASN7 ALA8 THR9 GLN10 GLN11 GLU12 GLU13 LEU14 ARG15 VAL16 ALA17 LEU18 VAL19 ASP20 GLY21 GLN22 ARG23 LEU24 TYR25 ASP26 LEU27 ASP28 ILE29 GLU30 SER31 PRO32 PHE119 ILE120 SER121 LEU122 ALA123 GLY124 SER125 TYR126 LEU127 VAL128 LEU129 MET130 PRO131 ASN132 ASN133 PRO134 ARG135 ALA136 GLY137 GLY138 ILE139 SER140 ARG141 ARG142 ILE143 GLU144 GLY145 ASP146 GLU150 LEU151 LYS152 GLU153 ALA154 LEU155 ALA156 SER157 LEU158 GLU159 LEU160 PRO161 GLU162 GLY163 MET164 GLY165 LEU166 ILE167 VAL168 ARG169 THR170 ALA171 GLY172 VAL173 GLY174 LYS175 SER176 ALA177 GLU178 ALA179 LEU180 GLN181 TRP182 ASP183 LEU184 SER185 PHE186 ARG187 LEU188 LYS189 HIS190 TRP191 GLU192 ALA193 ILE194 LYS195 LYS196 ALA197 ALA198 GLU199 SER200 ARG201 PRO202 ALA203 PRO204 PHE205 LEU206 ILE207 HIS208 GLN209 ASN212 VAL213 ILE214 VAL215 ARG216 ALA217 PHE218 ARG219 ASP220 TYR221 LEU222 ARG223 GLN224 ASP225 ILE226 GLY227 GLU228 ILE229 LEU230 ILE231 ASP232 ASN233 PRO234 LYS235 VAL236 LEU237 GLU238 LEU239 ALA240 ARG241 GLN242 HIS243 ILE244 ALA245 ALA246 LEU247 GLY248 ARG249 PRO250 ASP251 PHE252 SER253 SER254 LYS255 ILE256 LYS257 LEU258 TYR259 THR260 GLY261 GLU262 ILE263 PRO264 LEU265 PHE266 SER267 HIS268 TYR269 GLN270 ILE271 GLU272 SER273 GLN274 ILE275 GLU276 SER277 ALA278 PHE279 GLN280 ARG281 GLU282 VAL283 ARG284 LEU285 PRO286 SER287 GLY288 GLY289 SER290 ILE291 VAL292 ILE293 ASP294 SER295 THR296 GLU297 ALA298 LEU299 THR300 ALA301 ILE302 ASP303 ILE304 ASN305 SER306 ALA307 GLY313 ASP314 ILE315 GLU316 GLU317 THR318 ALA319 PHE320 ASN321 THR322 ASN323 LEU324 GLU325 ALA326 ALA327 ASP328 GLU329 ILE330 ALA331 ARG332 GLN333 LEU334 ARG335 LEU336 ARG337 ASP338 LEU339 GLY340 GLY341 LEU342 ILE343 VAL344 ILE345 ASP346 PHE347 ILE348 ASP349 MET350 THR351 PRO352 VAL353 ARG354 HIS355 GLN356 ARG357 ALA358 VAL359 GLU360 ASN361 ARG362 LEU363 ARG364 GLU365 ALA366 VAL367 ARG368 GLN369 ASP370 ARG371 ALA372 ARG373 ILE374 GLN375 ILE376 SER377 HIS378 ILE379 SER380 ARG381 PHE382 GLY383 LEU384 LEU385 GLU386 MET387 SER388 ARG389 GLN390 ARG391 LEU392 SER393 LEU396 GLY397 GLU398 SER399 SER400 HIS401 HIS402 VAL403 CYS404 PRO405 ARG406 CYS407 SER408 GLY409 THR410 GLY411 THR412 VAL413 ARG414 ASP415 ASN416 GLU417 SER418 LEU419 SER420 LEU421 SER422 ILE423 LEU424 ARG425 LEU426 ILE427 GLU428 GLU429 GLU430 ALA431 LEU432 LYS433 GLU434 ASN435 THR436 GLN437 GLU438 VAL439 HIS440 ALA441 ILE442 VAL443 PRO444 VAL445 PRO446 ILE447 ALA448 SER449 TYR450 LEU451 LEU452 ASN453 GLU454 LYS455 ARG456 SER457 ALA458 VAL459 ASN460 ALA461 ILE462 GLU463 THR464 ARG465 GLN466 ASP467 GLY468 VAL469 ARG470 CYS471 VAL472 ILE473 VAL474 PRO475 ASN476 ASP477 GLN478 MET479 GLU480 THR481 PRO482 HIS483 TYR484 HIS485 VAL486 LEU487 ARG488 VAL489 ARG490 LYS491 GLY492 GLU493 GLU494 THR495 PRO496 THR497 LEU498 SER499 TYR500 MET501 LEU502 PRO503 LYS504 LEU505 HIS506 GLU507 GLU508 ALA509
Unit 4 MET1 LYS2 ARG3 MET4 LEU5 ILE6 ASN7 ALA8 THR9 GLN10 GLN11 GLU12 GLU13 LEU14 ARG15 VAL16 ALA17 LEU18 VAL19 ASP20 GLY21 GLN22 ARG23 LEU24 TYR25 ASP26 LEU27 ASP28 ILE29 GLU30 SER31 PRO32 GLU35 GLN36 LYS37 LYS38 ALA39 ASN40 ILE41 TYR42 LYS43 GLY44 LYS45 ILE46 THR47 ARG48 ILE49 GLU50 PRO51 SER52 LEU53 GLU54 ALA55 ALA56 PHE57 VAL58 ASP59 TYR60 GLY61 ALA62 GLU63 ARG64 HIS65 GLY66 PHE67 LEU68 PRO69 LEU70 LYS71 GLU72 ILE73 ALA74 ARG75 GLU76 TYR77 PHE78 PRO79 ARG87 PRO88 ASN89 ILE90 LYS91 ASP92 VAL93 LEU94 ARG95 GLU96 GLY97 GLN98 GLU99 VAL100 ILE101 VAL102 GLN103 ILE104 ASP105 LYS106 GLU107 GLU108 ARG109 GLY110 ASN111 LYS112 GLY113 ALA114 ALA115 LEU116 THR117 THR118 PHE119 ILE120 SER121 LEU122 ALA123 GLY124 SER125 TYR126 LEU127 VAL128 LEU129 MET130 PRO131 ASN132 ASN133 PRO134 ARG135 ALA136 GLY137 GLY138 ILE139 SER140 ARG141 ARG142 ILE143 GLU144 ASP146 ASP147 ARG148 THR149 GLU150 LEU151 LYS152 GLU153 ALA154 LEU155 ALA156 SER157 LEU158 GLU159 LEU160 PRO161 GLU162 GLY163 MET164 GLY165 LEU166 ILE167 VAL168 ARG169 THR170 ALA171 GLY172 VAL173 GLY174 LYS175 SER176 ALA177 GLU178 ALA179 LEU180 GLN181 TRP182 ASP183 LEU184 SER185 PHE186 ARG187 LEU188 LYS189 HIS190 TRP191 GLU192 ALA193 ILE194 LYS195 LYS196 ALA197 ALA198 GLU199 SER200 ARG201 PRO202 ALA203 PRO204 PHE205 LEU206 ILE207 HIS208 GLN209 GLU210 SER211 ASN212 VAL213 ILE214 VAL215 ARG216 ALA217 PHE218 ARG219 ASP220 TYR221 LEU222 ARG223 GLN224 ASP225 ILE226 GLY227 GLU228 ILE229 LEU230 ILE231 ASP232 ASN233 PRO234 LYS235 VAL236 LEU237 GLU238 LEU239 ALA240 ARG241 GLN242 HIS243 ILE244 ALA245 ALA246 LEU247 GLY248 ARG249 PRO250 ASP251 PHE252 SER253 SER254 LYS255 ILE256 LYS257 LEU258 TYR259 THR260 GLY261 GLU262 ILE263 PRO264 LEU265 PHE266 SER267 HIS268 TYR269 GLN270 ILE271 GLU272 SER273 GLN274 ILE275 GLU276 SER277 ALA278 PHE279 GLN280 ARG281 GLU282 VAL283 ARG284 LEU285 PRO286 SER287 GLY288 GLY289 SER290 ILE291 VAL292 ILE293 ASP294 SER295 THR296 GLU297 ALA298 LEU299 THR300 ALA301 ILE302 ASP303 ILE304 ASN305 SER306 ALA307 ARG308 ASP314 ILE315 GLU316 GLU317 THR318 ALA319 PHE320 ASN321 THR322 ASN323 LEU324 GLU325 ALA326 ALA327 ASP328 GLU329 ILE330 ALA331 ARG332 GLN333 LEU334 ARG335 LEU336 ARG337 ASP338 LEU339 GLY340 GLY341 LEU342 ILE343 VAL344 ILE345 ASP346 PHE347 ILE348 ASP349 MET350 THR351 PRO352 VAL353 ARG354 HIS355 GLN356 ARG357 ALA358 VAL359 GLU360 ASN361 ARG362 LEU363 ARG364 GLU365 ALA366 VAL367 ARG368 GLN369 ASP370 ARG371 ALA372 ARG373 ILE374 GLN375 ILE376 SER377 HIS378 ILE379 SER380 ARG381 PHE382 GLY383 LEU384 LEU385 GLU386 MET387 SER388 ARG389 GLN390 ARG391 LEU392 SER399 SER400 HIS401 HIS402 VAL403 CYS404 PRO405 ARG406 CYS407 SER408 GLY409 THR410 GLY411 THR412 VAL413 ARG414 ASP415 ASN416 GLU417 SER418 LEU419 SER420 LEU421 SER422 ILE423 LEU424 ARG425 LEU426 ILE427 GLU428 GLU429 GLU430 ALA431 LEU432 LYS433 GLU434 ASN435 THR436 GLN437 GLU438 VAL439 HIS440 ALA441 ILE442 VAL443 PRO444 VAL445 PRO446 ILE447 ALA448 SER449 TYR450 LEU451 LEU452 ASN453 GLU454 LYS455 ARG456 SER457 ALA458 VAL459 ASN460 ALA461 ILE462 GLU463 THR464 ARG465 GLN466 ASP467 GLY468 VAL469 ARG470 CYS471 VAL472 ILE473 VAL474 PRO475 ASN476 ASP477 GLN478 MET479 GLU480 THR481 PRO482 HIS483 TYR484 HIS485 VAL486 LEU487 ARG488 VAL489 ARG490 LYS491 GLY492 GLU493 GLU494 THR495 PRO496 THR497 LEU498 SER499 TYR500 MET501 LEU502 PRO503 LYS504 LEU505 HIS506 GLU507 GLU508
Nucleic acids
Unit 5 U1 U2
Unit 6 U1 U2
Unit 7 U1 U2 G3
Unit 8 U1 U2 G3
Ligands
Unit 9 ZN1506
Unit 10 ZN1509
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany