HEADER TRANSFERASE 26-OCT-18 6I0T TITLE CRYSTAL STRUCTURE OF DMTAILOR IN COMPLEX WITH GPU COMPND MOL_ID: 1; COMPND 2 MOLECULE: TERMINAL URIDYLYLTRANSFERASE TAILOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TUTASE TAILOR; COMPND 5 EC: 2.7.7.52; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*GP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: TAILOR, CG1091; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 11 ORGANISM_TAXID: 7227 KEYWDS TERMINAL URIDYL TRANSFERASE, NUCLEOTIDYL TRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KROUPOVA,A.IVASCU,M.JINEK REVDAT 3 24-JAN-24 6I0T 1 REMARK REVDAT 2 06-FEB-19 6I0T 1 JRNL REVDAT 1 05-DEC-18 6I0T 0 JRNL AUTH A.KROUPOVA,A.IVASCU,M.M.REIMAO-PINTO,S.L.AMERES,M.JINEK JRNL TITL STRUCTURAL BASIS FOR ACCEPTOR RNA SUBSTRATE SELECTIVITY OF JRNL TITL 2 THE 3' TERMINAL URIDYLYL TRANSFERASE TAILOR. JRNL REF NUCLEIC ACIDS RES. V. 47 1030 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30462292 JRNL DOI 10.1093/NAR/GKY1164 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3211: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24045 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.9879 - 4.1591 1.00 2719 146 0.1717 0.1985 REMARK 3 2 4.1591 - 3.3016 1.00 2579 136 0.1724 0.2122 REMARK 3 3 3.3016 - 2.8843 1.00 2531 129 0.2279 0.2509 REMARK 3 4 2.8843 - 2.6206 1.00 2504 135 0.2244 0.2599 REMARK 3 5 2.6206 - 2.4328 1.00 2526 135 0.2507 0.3006 REMARK 3 6 2.4328 - 2.2894 1.00 2509 131 0.2536 0.2480 REMARK 3 7 2.2894 - 2.1747 1.00 2486 132 0.2670 0.3027 REMARK 3 8 2.1747 - 2.0801 1.00 2466 133 0.2921 0.3036 REMARK 3 9 2.0801 - 2.0000 1.00 2513 135 0.3258 0.3286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2925 REMARK 3 ANGLE : 0.865 3968 REMARK 3 CHIRALITY : 0.057 451 REMARK 3 PLANARITY : 0.005 495 REMARK 3 DIHEDRAL : 20.950 1096 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24045 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 18.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.38000 REMARK 200 FOR SHELL : 1.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6I0S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) GLYCEROL ETHOXYLATE, 60 MM REMARK 280 SODIUM MALONATE, PH7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.09467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.18933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.18933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.09467 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 177 REMARK 465 ASN A 178 REMARK 465 ALA A 179 REMARK 465 PRO A 180 REMARK 465 VAL A 181 REMARK 465 GLN A 182 REMARK 465 PRO A 183 REMARK 465 HIS A 184 REMARK 465 PRO A 185 REMARK 465 THR A 186 REMARK 465 HIS A 187 REMARK 465 GLN A 188 REMARK 465 THR A 189 REMARK 465 LYS A 190 REMARK 465 GLN A 191 REMARK 465 GLU A 192 REMARK 465 LYS A 193 REMARK 465 LYS A 194 REMARK 465 GLN A 195 REMARK 465 ALA A 196 REMARK 465 GLN A 197 REMARK 465 ALA A 417 REMARK 465 ALA A 418 REMARK 465 ASN A 419 REMARK 465 GLU A 549 REMARK 465 PRO A 550 REMARK 465 SER A 551 REMARK 465 THR A 552 REMARK 465 ASN A 553 REMARK 465 TRP A 554 REMARK 465 ARG A 555 REMARK 465 GLN A 556 REMARK 465 ARG A 557 REMARK 465 TYR A 558 REMARK 465 ALA A 559 REMARK 465 PHE A 560 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6I0S RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT SUBSTRATE BOUND. REMARK 900 BELONGS TO THE SAME PUBLICATION. REMARK 900 RELATED ID: 6I0U RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT SUBSTRATE BOUND. REMARK 900 BELONGS TO THE SAME PUBLICATION. REMARK 900 RELATED ID: 6I0V RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT SUBSTRATE BOUND. REMARK 900 BELONGS TO THE SAME PUBLICATION. DBREF 6I0T A 180 560 UNP Q9VI58 TUTT_DROME 180 560 DBREF 6I0T B 1 2 PDB 6I0T 6I0T 1 2 SEQADV 6I0T SER A 177 UNP Q9VI58 EXPRESSION TAG SEQADV 6I0T ASN A 178 UNP Q9VI58 EXPRESSION TAG SEQADV 6I0T ALA A 179 UNP Q9VI58 EXPRESSION TAG SEQRES 1 A 384 SER ASN ALA PRO VAL GLN PRO HIS PRO THR HIS GLN THR SEQRES 2 A 384 LYS GLN GLU LYS LYS GLN ALA GLN VAL LYS ALA ARG GLN SEQRES 3 A 384 HIS ILE THR VAL ARG LEU PRO LYS LYS ALA ARG ALA MET SEQRES 4 A 384 ILE VAL GLY GLU ILE THR ASN VAL PHE LYS ASP LYS TYR SEQRES 5 A 384 PRO ILE ALA ASP LYS LEU LYS VAL ILE PRO GLU TYR ASP SEQRES 6 A 384 VAL ILE GLU GLN ASP LEU CYS LYS LEU LEU SER PRO GLY SEQRES 7 A 384 PHE PRO LYS GLN PRO LEU ARG VAL TYR LYS PHE GLY SER SEQRES 8 A 384 ARG ILE THR GLY ILE GLY ASN ARG SER SER ASP LEU ASP SEQRES 9 A 384 LEU PHE VAL ASP ILE GLY ASN THR PHE HIS THR PHE GLU SEQRES 10 A 384 HIS ARG ALA SER ASN ALA THR VAL ALA LYS LEU ARG ALA SEQRES 11 A 384 MET ARG LYS PHE PHE CYS ASP SER GLU ASP TRP ARG LEU SEQRES 12 A 384 ILE ASN PHE ILE GLU GLN ALA ARG VAL PRO ILE ILE LYS SEQRES 13 A 384 THR CYS HIS LEU PRO THR GLY ILE GLU CYS ASP ILE CYS SEQRES 14 A 384 LEU ASN SER MET GLY PHE CYS ASN THR ASN LEU LEU LYS SEQRES 15 A 384 TYR ILE PHE GLU SER GLN PRO LEU THR GLN TYR MET CYS SEQRES 16 A 384 ILE TYR VAL LYS ASN TRP LEU GLU ARG CYS LYS LEU THR SEQRES 17 A 384 GLU GLN ILE SER THR TYR SER ILE THR LEU MET VAL ILE SEQRES 18 A 384 TYR PHE LEU GLN LEU GLN ALA LEU LEU PRO PRO ILE ALA SEQRES 19 A 384 MET LEU GLN ILE GLU ASP ALA ALA ASN GLN ALA VAL LEU SEQRES 20 A 384 VAL GLY PRO TRP VAL VAL ASN PHE ALA GLN LYS SER PHE SEQRES 21 A 384 SER GLU LEU GLY LEU GLN GLN LEU LYS ALA THR VAL PRO SEQRES 22 A 384 VAL ILE LYS GLY PHE LEU ARG ASN PHE PHE ALA TYR PHE SEQRES 23 A 384 ALA LYS PHE ASP TYR GLU HIS PHE LEU VAL CYS PRO TYR SEQRES 24 A 384 ILE GLY GLN ALA ASN VAL GLU ILE ALA LYS ILE GLU ARG SEQRES 25 A 384 MET LEU HIS ALA ARG TYR SER ALA TYR VAL SER ASP ASN SEQRES 26 A 384 PRO GLU CYS SER ILE GLN LEU LYS LYS PRO MET VAL VAL SEQRES 27 A 384 GLN ASP PRO ILE GLN LEU ASN HIS ASN VAL THR LYS ALA SEQRES 28 A 384 VAL THR LYS TYR GLY LEU GLN THR PHE VAL ASP TYR CYS SEQRES 29 A 384 GLN GLN THR ALA GLU LEU LEU GLU GLU PRO SER THR ASN SEQRES 30 A 384 TRP ARG GLN ARG TYR ALA PHE SEQRES 1 B 2 G U FORMUL 3 HOH *91(H2 O) HELIX 1 AA1 PRO A 209 GLY A 218 1 10 HELIX 2 AA2 ILE A 220 ASP A 226 1 7 HELIX 3 AA3 ASP A 226 LEU A 234 1 9 HELIX 4 AA4 ILE A 237 SER A 252 1 16 HELIX 5 AA5 GLY A 266 GLY A 271 1 6 HELIX 6 AA6 SER A 297 SER A 314 1 18 HELIX 7 AA7 SER A 348 GLN A 364 1 17 HELIX 8 AA8 GLN A 364 CYS A 381 1 18 HELIX 9 AA9 SER A 388 GLN A 403 1 16 HELIX 10 AB1 PRO A 408 GLN A 413 5 6 HELIX 11 AB2 SER A 435 GLY A 440 5 6 HELIX 12 AB3 THR A 447 PHE A 465 1 19 HELIX 13 AB4 LYS A 485 LEU A 490 1 6 HELIX 14 AB5 HIS A 491 ASN A 501 1 11 HELIX 15 AB6 PRO A 502 SER A 505 5 4 HELIX 16 AB7 THR A 529 LEU A 547 1 19 SHEET 1 AA1 5 LEU A 260 PHE A 265 0 SHEET 2 AA1 5 LEU A 279 ILE A 285 -1 O ASP A 284 N ARG A 261 SHEET 3 AA1 5 GLU A 341 CYS A 345 1 O ASP A 343 N LEU A 281 SHEET 4 AA1 5 ILE A 330 HIS A 335 -1 N THR A 333 O CYS A 342 SHEET 5 AA1 5 TRP A 317 ILE A 323 -1 N ILE A 320 O LYS A 332 SHEET 1 AA2 2 LEU A 423 VAL A 424 0 SHEET 2 AA2 2 TRP A 427 VAL A 428 -1 O TRP A 427 N VAL A 424 CRYST1 60.425 60.425 162.284 90.00 90.00 120.00 P 31 2 1 6 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 0.016549 0.009555 0.000000 0.00000 SCALE2 0.000000 0.019110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006162 0.00000