PDB Short entry for 7R9F HEADER RNA BINDING PROTEIN/RNA 29-JUN-21 7R9F TITLE WILD-TYPE YEAST PSEUDOURIDINE SYNTHASE, PUS1, BOUND TO 5-FLUOROURACIL TITLE 2 RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA PSEUDOURIDINE SYNTHASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRNA PSEUDOURIDYLATE SYNTHASE 1,TRNA-URIDINE ISOMERASE 1; COMPND 5 EC: 5.4.99.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'- COMPND 9 R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PUS1, YPL212C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS PSEUDOURIDINE, PUS, PUS1, RNA, SYNTHASE, MRNA, YEAST, PSEUDO URACIL, KEYWDS 2 PSEUDOURACIL, URACIL, SACCHAROMYCES CEREVISIAE, INACTIVE, KEYWDS 3 CATALYTICALLY INACTIVE, DEAD, PSEUDOURIDINE SYNTHASE, RNA BINDING KEYWDS 4 PROTEIN, 5-FLUOROURACIL, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.A.DOYLE,B.L.STODDARD REVDAT 3 15-NOV-23 7R9F 1 JRNL REVDAT 2 18-OCT-23 7R9F 1 REMARK REVDAT 1 15-DEC-21 7R9F 0 JRNL AUTH S.GRUNBERG,L.A.DOYLE,E.J.WOLF,N.DAI,I.R.CORREA JR.,E.YIGIT, JRNL AUTH 2 B.L.STODDARD JRNL TITL THE STRUCTURAL BASIS OF MRNA RECOGNITION AND BINDING BY JRNL TITL 2 YEAST PSEUDOURIDINE SYNTHASE PUS1. JRNL REF PLOS ONE V. 18 91267 2023 JRNL REFN ESSN 1932-6203 JRNL PMID 37939088 JRNL DOI 10.1371/JOURNAL.PONE.0291267 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1950 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 46.8800 - 6.9600 1.00 1393 155 0.2269 0.2563 REMARK 3 2 6.9500 - 5.5300 1.00 1298 145 0.2616 0.2740 REMARK 3 3 5.5300 - 4.8300 1.00 1266 141 0.2355 0.2908 REMARK 3 4 4.8300 - 4.3900 1.00 1268 140 0.1999 0.2312 REMARK 3 5 4.3900 - 4.0700 1.00 1236 138 0.2333 0.2817 REMARK 3 6 4.0700 - 3.8300 1.00 1249 138 0.2453 0.2817 REMARK 3 7 3.8300 - 3.6400 1.00 1232 137 0.2680 0.3324 REMARK 3 8 3.6400 - 3.4800 1.00 1252 140 0.2822 0.3102 REMARK 3 9 3.4800 - 3.3500 1.00 1215 134 0.3010 0.3476 REMARK 3 10 3.3500 - 3.2300 1.00 1237 138 0.2919 0.3410 REMARK 3 11 3.2300 - 3.1300 1.00 1222 136 0.3043 0.3917 REMARK 3 12 3.1300 - 3.0400 1.00 1232 136 0.3230 0.3828 REMARK 3 13 3.0400 - 2.9600 1.00 1218 136 0.3634 0.4252 REMARK 3 14 2.9600 - 2.8900 1.00 1222 136 0.4060 0.4178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.82 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 : 0.003 3069 REMARK 3 ANGLE : 0.533 4235 REMARK 3 CHIRALITY : 0.038 481 REMARK 3 PLANARITY : 0.003 506 REMARK 3 DIHEDRAL : 17.115 546 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 7R9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000257634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.890 REMARK 200 RESOLUTION RANGE LOW (A) : 48.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 38.20 REMARK 200 R MERGE (I) : 0.25200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 40.10 REMARK 200 R MERGE FOR SHELL (I) : 4.91200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 4J37 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE, 18% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 52.71000 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 105.42000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.06500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 131.77500 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 26.35500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.71000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 105.42000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 131.77500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 79.06500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.35500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 LEU A 6 REMARK 465 ARG A 7 REMARK 465 PRO A 8 REMARK 465 ALA A 9 REMARK 465 TYR A 10 REMARK 465 ASP A 11 REMARK 465 ASP A 12 REMARK 465 GLN A 13 REMARK 465 VAL A 14 REMARK 465 ASN A 15 REMARK 465 GLU A 16 REMARK 465 ASP A 17 REMARK 465 VAL A 18 REMARK 465 TYR A 19 REMARK 465 LYS A 20 REMARK 465 ARG A 21 REMARK 465 GLY A 22 REMARK 465 ALA A 23 REMARK 465 GLN A 24 REMARK 465 SER A 25 REMARK 465 LYS A 26 REMARK 465 LEU A 27 REMARK 465 THR A 28 REMARK 465 LYS A 29 REMARK 465 ALA A 30 REMARK 465 ARG A 31 REMARK 465 LYS A 32 REMARK 465 ALA A 33 REMARK 465 ASP A 34 REMARK 465 PHE A 35 REMARK 465 ASP A 36 REMARK 465 ASP A 37 REMARK 465 GLU A 38 REMARK 465 LYS A 39 REMARK 465 ASP A 40 REMARK 465 LYS A 41 REMARK 465 LYS A 42 REMARK 465 LYS A 43 REMARK 465 ASP A 44 REMARK 465 ASN A 45 REMARK 465 ASP A 46 REMARK 465 LYS A 47 REMARK 465 HIS A 48 REMARK 465 ILE A 49 REMARK 465 ASP A 50 REMARK 465 LYS A 51 REMARK 465 ARG A 52 REMARK 465 PRO A 53 REMARK 465 LYS A 54 REMARK 465 SER A 55 REMARK 465 GLY A 56 REMARK 465 PRO A 57 REMARK 465 ARG A 58 REMARK 465 LEU A 59 REMARK 465 ASP A 60 REMARK 465 GLU A 61 REMARK 465 ASN A 62 REMARK 465 GLY A 63 REMARK 465 ASN A 64 REMARK 465 PRO A 65 REMARK 465 LEU A 66 REMARK 465 PRO A 67 REMARK 465 LYS A 68 REMARK 465 GLU A 69 REMARK 465 PRO A 70 REMARK 465 ARG A 71 REMARK 465 ASN A 120 REMARK 465 ASP A 121 REMARK 465 LEU A 122 REMARK 465 LYS A 123 REMARK 465 LYS A 124 REMARK 465 ASN A 125 REMARK 465 GLY A 126 REMARK 465 PRO A 220 REMARK 465 GLY A 221 REMARK 465 VAL A 222 REMARK 465 ALA A 254 REMARK 465 TYR A 255 REMARK 465 VAL A 256 REMARK 465 PRO A 257 REMARK 465 PRO A 258 REMARK 465 ALA A 259 REMARK 465 ARG A 260 REMARK 465 ASP A 261 REMARK 465 GLU A 262 REMARK 465 PHE A 263 REMARK 465 ASP A 264 REMARK 465 ILE A 265 REMARK 465 ASN A 266 REMARK 465 ASN A 464 REMARK 465 LYS A 465 REMARK 465 VAL A 466 REMARK 465 THR A 467 REMARK 465 GLY A 468 REMARK 465 ALA A 469 REMARK 465 GLN A 470 REMARK 465 GLY A 471 REMARK 465 GLU A 472 REMARK 465 GLU A 473 REMARK 465 THR A 474 REMARK 465 ALA A 475 REMARK 465 ASP A 476 REMARK 465 LYS A 477 REMARK 465 SER A 478 REMARK 465 GLY A 479 REMARK 465 PRO A 480 REMARK 465 ALA A 481 REMARK 465 VAL A 482 REMARK 465 GLN A 483 REMARK 465 GLY A 494 REMARK 465 ILE A 495 REMARK 465 PRO A 496 REMARK 465 GLY A 497 REMARK 465 LEU A 498 REMARK 465 THR A 499 REMARK 465 ASP A 500 REMARK 465 ALA A 501 REMARK 465 PRO A 502 REMARK 465 GLU A 503 REMARK 465 SER A 504 REMARK 465 ASN A 505 REMARK 465 LYS A 506 REMARK 465 LYS A 507 REMARK 465 ILE A 508 REMARK 465 LYS A 509 REMARK 465 GLN A 510 REMARK 465 ARG A 511 REMARK 465 LYS A 512 REMARK 465 ARG A 513 REMARK 465 MET A 514 REMARK 465 GLU A 515 REMARK 465 GLU A 516 REMARK 465 GLU A 517 REMARK 465 GLU A 518 REMARK 465 ALA A 519 REMARK 465 ALA A 520 REMARK 465 SER A 521 REMARK 465 LYS A 522 REMARK 465 LYS A 523 REMARK 465 ALA A 524 REMARK 465 GLU A 525 REMARK 465 ILE A 526 REMARK 465 SER A 527 REMARK 465 SER A 528 REMARK 465 THR A 529 REMARK 465 THR A 530 REMARK 465 GLN A 531 REMARK 465 SER A 532 REMARK 465 ASN A 533 REMARK 465 GLU A 534 REMARK 465 PRO A 535 REMARK 465 GLU A 536 REMARK 465 VAL A 537 REMARK 465 GLN A 538 REMARK 465 PRO A 539 REMARK 465 GLU A 540 REMARK 465 ALA A 541 REMARK 465 ALA A 542 REMARK 465 ALA A 543 REMARK 465 ASN A 544 REMARK 465 G B 14 REMARK 465 G B 15 REMARK 465 A B 16 REMARK 465 U B 17 REMARK 465 A B 18 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 72 CD1 CD2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 ARG A 75 NE CZ NH1 NH2 REMARK 470 THR A 86 CG2 REMARK 470 LYS A 106 CD CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 ILE A 114 CG1 CG2 CD1 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 ASP A 117 CG OD1 OD2 REMARK 470 ASN A 118 CG OD1 ND2 REMARK 470 SER A 119 OG REMARK 470 MET A 128 CG SD CE REMARK 470 ASP A 134 OD1 OD2 REMARK 470 ILE A 144 CD1 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 ILE A 149 CG1 CG2 CD1 REMARK 470 ILE A 150 CG1 CG2 CD1 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 ASP A 152 CG OD1 OD2 REMARK 470 ASP A 154 CG OD1 OD2 REMARK 470 GLN A 157 CG CD OE1 NE2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 GLU A 173 CG CD OE1 OE2 REMARK 470 ARG A 174 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 177 CG CD CE NZ REMARK 470 ARG A 182 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 SER A 187 OG REMARK 470 LYS A 203 CG CD CE NZ REMARK 470 SER A 206 OG REMARK 470 ILE A 207 CG1 CG2 CD1 REMARK 470 ARG A 210 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 212 CG1 CG2 CD1 REMARK 470 GLU A 214 CG CD OE1 OE2 REMARK 470 SER A 215 OG REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 LEU A 219 CG CD1 CD2 REMARK 470 LEU A 223 CG CD1 CD2 REMARK 470 LEU A 227 CG CD1 CD2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 GLU A 234 CG CD OE1 OE2 REMARK 470 LYS A 238 CE NZ REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 LYS A 243 CD CE NZ REMARK 470 PHE A 244 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 245 OG REMARK 470 GLU A 248 CD OE1 OE2 REMARK 470 ILE A 249 CG1 CG2 CD1 REMARK 470 GLU A 250 CG CD OE1 OE2 REMARK 470 ILE A 252 CG1 CG2 CD1 REMARK 470 LEU A 253 CG CD1 CD2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 LEU A 269 CG CD1 CD2 REMARK 470 TYR A 270 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 277 CG CD CE NZ REMARK 470 ARG A 286 CG CD NE CZ NH1 NH2 REMARK 470 THR A 301 CG2 REMARK 470 SER A 302 OG REMARK 470 LEU A 315 CG CD1 CD2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 ASP A 318 CG OD1 OD2 REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 GLU A 321 CG CD OE1 OE2 REMARK 470 SER A 323 OG REMARK 470 ILE A 325 CG2 CD1 REMARK 470 LYS A 329 CD CE NZ REMARK 470 ASP A 330 CG OD1 OD2 REMARK 470 ILE A 331 CG2 CD1 REMARK 470 LYS A 332 CD CE NZ REMARK 470 VAL A 333 CG1 REMARK 470 ASP A 335 OD1 OD2 REMARK 470 ILE A 339 CD1 REMARK 470 ASP A 341 CG OD1 OD2 REMARK 470 THR A 344 CG2 REMARK 470 ILE A 351 CD1 REMARK 470 LEU A 358 CG CD1 CD2 REMARK 470 CYS A 376 SG REMARK 470 GLU A 379 CG CD OE1 OE2 REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 383 CD OE1 NE2 REMARK 470 GLN A 387 CG CD OE1 NE2 REMARK 470 GLN A 388 CD OE1 NE2 REMARK 470 LYS A 389 CD CE NZ REMARK 470 ILE A 390 CD1 REMARK 470 ASN A 391 OD1 ND2 REMARK 470 ILE A 392 CD1 REMARK 470 GLU A 403 CD OE1 OE2 REMARK 470 VAL A 406 CG1 CG2 REMARK 470 LYS A 412 CG CD CE NZ REMARK 470 LEU A 414 CG CD1 CD2 REMARK 470 GLU A 415 CG CD OE1 OE2 REMARK 470 LYS A 420 CD CE NZ REMARK 470 SER A 425 OG REMARK 470 LYS A 426 CG CD CE NZ REMARK 470 ASP A 429 CG OD1 OD2 REMARK 470 GLU A 430 CG CD OE1 OE2 REMARK 470 ASP A 432 CG OD1 OD2 REMARK 470 LYS A 433 CG CD CE NZ REMARK 470 LYS A 435 CE NZ REMARK 470 MET A 436 SD CE REMARK 470 LYS A 437 CD CE NZ REMARK 470 ASP A 441 CG OD1 OD2 REMARK 470 LYS A 442 CD CE NZ REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 GLU A 446 CD OE1 OE2 REMARK 470 VAL A 448 CG2 REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 VAL A 452 CG2 REMARK 470 SER A 458 OG REMARK 470 SER A 462 OG REMARK 470 PHE A 463 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 SER A 485 OG REMARK 470 ILE A 486 CG1 CG2 CD1 REMARK 470 PHE A 487 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 488 CG CD OE1 OE2 REMARK 470 PHE A 489 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 490 CG CD1 CD2 REMARK 470 THR A 491 OG1 CG2 REMARK 470 LYS A 493 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 394 OP2 G B 6 8555 2.17 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 HIS A 89 43.96 -99.56 REMARK 500 SER A 115 -76.45 -82.87 REMARK 500 LYS A 116 -152.37 179.50 REMARK 500 ASP A 117 -116.65 57.66 REMARK 500 ASP A 154 73.79 -110.96 REMARK 500 GLU A 248 72.08 -69.31 REMARK 500 GLU A 250 49.11 -91.67 REMARK 500 GLU A 268 -38.82 173.35 REMARK 500 PHE A 310 43.23 -106.64 REMARK 500 ASP A 318 -148.84 -92.66 REMARK 500 LYS A 320 37.84 -69.90 REMARK 500 GLN A 387 -70.15 -48.61 REMARK 500 ILE A 439 -61.18 -97.48 REMARK 500 ASP A 449 -66.64 -93.58 REMARK 500 PHE A 489 37.89 -95.16 REMARK 500 THR A 491 18.65 59.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 7R9F A 1 544 UNP Q12211 PUS1_YEAST 1 544 DBREF 7R9F B 1 18 PDB 7R9F 7R9F 1 18 SEQRES 1 A 544 MET SER GLU GLU ASN LEU ARG PRO ALA TYR ASP ASP GLN SEQRES 2 A 544 VAL ASN GLU ASP VAL TYR LYS ARG GLY ALA GLN SER LYS SEQRES 3 A 544 LEU THR LYS ALA ARG LYS ALA ASP PHE ASP ASP GLU LYS SEQRES 4 A 544 ASP LYS LYS LYS ASP ASN ASP LYS HIS ILE ASP LYS ARG SEQRES 5 A 544 PRO LYS SER GLY PRO ARG LEU ASP GLU ASN GLY ASN PRO SEQRES 6 A 544 LEU PRO LYS GLU PRO ARG LEU PRO LYS ARG LYS VAL ALA SEQRES 7 A 544 VAL MET VAL GLY TYR CYS GLY THR GLY TYR HIS GLY MET SEQRES 8 A 544 GLN TYR ASN PRO PRO ASN PRO THR ILE GLU SER ALA LEU SEQRES 9 A 544 PHE LYS ALA PHE VAL GLU ALA GLY ALA ILE SER LYS ASP SEQRES 10 A 544 ASN SER ASN ASP LEU LYS LYS ASN GLY PHE MET ARG ALA SEQRES 11 A 544 ALA ARG THR ASP LYS GLY VAL HIS ALA GLY GLY ASN LEU SEQRES 12 A 544 ILE SER LEU LYS MET ILE ILE GLU ASP PRO ASP ILE LYS SEQRES 13 A 544 GLN LYS ILE ASN GLU LYS LEU PRO GLU GLY ILE ARG VAL SEQRES 14 A 544 TRP ASP ILE GLU ARG VAL ASN LYS ALA PHE ASP CYS ARG SEQRES 15 A 544 LYS MET CYS SER SER ARG TRP TYR GLU TYR LEU LEU PRO SEQRES 16 A 544 THR TYR SER LEU ILE GLY PRO LYS PRO GLY SER ILE LEU SEQRES 17 A 544 TYR ARG ASP ILE GLU GLU SER LYS THR GLU LEU PRO GLY SEQRES 18 A 544 VAL LEU ASP GLU ASP LEU GLU SER LYS GLU PHE TRP GLU SEQRES 19 A 544 GLU PHE LYS LYS ASP ALA ASN GLU LYS PHE SER THR GLU SEQRES 20 A 544 GLU ILE GLU ALA ILE LEU ALA TYR VAL PRO PRO ALA ARG SEQRES 21 A 544 ASP GLU PHE ASP ILE ASN GLU GLU LEU TYR GLN LYS VAL SEQRES 22 A 544 LYS LYS TYR LYS GLN LEU GLU ASN ALA HIS ARG ARG ARG SEQRES 23 A 544 TYR ARG ILE SER ALA ALA LYS LEU ALA LYS PHE ARG ALA SEQRES 24 A 544 SER THR SER GLN TYR LEU GLY ALA HIS ASN PHE HIS ASN SEQRES 25 A 544 PHE THR LEU GLY LYS ASP PHE LYS GLU PRO SER ALA ILE SEQRES 26 A 544 ARG PHE MET LYS ASP ILE LYS VAL SER ASP PRO PHE VAL SEQRES 27 A 544 ILE GLY ASP ALA GLN THR GLU TRP ILE SER ILE LYS ILE SEQRES 28 A 544 HIS GLY GLN SER PHE MET LEU HIS GLN ILE ARG LYS MET SEQRES 29 A 544 VAL SER MET ALA THR LEU ILE THR ARG CYS GLY CYS PRO SEQRES 30 A 544 VAL GLU ARG ILE SER GLN ALA TYR GLY GLN GLN LYS ILE SEQRES 31 A 544 ASN ILE PRO LYS ALA PRO ALA LEU GLY LEU LEU LEU GLU SEQRES 32 A 544 ALA PRO VAL PHE GLU GLY TYR ASN LYS ARG LEU GLU GLN SEQRES 33 A 544 PHE GLY TYR LYS ALA ILE ASP PHE SER LYS TYR GLN ASP SEQRES 34 A 544 GLU VAL ASP LYS PHE LYS MET LYS HIS ILE TYR ASP LYS SEQRES 35 A 544 ILE TYR LYS GLU GLU VAL ASP GLU ASN VAL PHE ASN ALA SEQRES 36 A 544 PHE PHE SER TYR ILE ASP SER PHE ASN LYS VAL THR GLY SEQRES 37 A 544 ALA GLN GLY GLU GLU THR ALA ASP LYS SER GLY PRO ALA SEQRES 38 A 544 VAL GLN LYS SER ILE PHE GLU PHE LEU THR ALA LYS GLY SEQRES 39 A 544 ILE PRO GLY LEU THR ASP ALA PRO GLU SER ASN LYS LYS SEQRES 40 A 544 ILE LYS GLN ARG LYS ARG MET GLU GLU GLU GLU ALA ALA SEQRES 41 A 544 SER LYS LYS ALA GLU ILE SER SER THR THR GLN SER ASN SEQRES 42 A 544 GLU PRO GLU VAL GLN PRO GLU ALA ALA ALA ASN SEQRES 1 B 18 5UD A A U C G G G A U U C C SEQRES 2 B 18 G G A U A HET 5UD B 1 18 HET SO4 A 601 5 HETNAM 5UD 5-FLUOROURIDINE HETNAM SO4 SULFATE ION FORMUL 2 5UD C9 H11 F N2 O6 FORMUL 3 SO4 O4 S 2- HELIX 1 AA1 THR A 99 GLY A 112 1 14 HELIX 2 AA2 ILE A 155 LYS A 162 1 8 HELIX 3 AA3 TYR A 197 ILE A 200 5 4 HELIX 4 AA4 SER A 206 SER A 215 1 10 HELIX 5 AA5 LEU A 227 PHE A 244 1 18 HELIX 6 AA6 GLU A 268 ARG A 286 1 19 HELIX 7 AA7 SER A 290 TYR A 304 1 15 HELIX 8 AA8 HIS A 311 THR A 314 5 4 HELIX 9 AA9 HIS A 359 GLY A 375 1 17 HELIX 10 AB1 GLU A 379 TYR A 385 1 7 HELIX 11 AB2 PRO A 396 LEU A 398 5 3 HELIX 12 AB3 PHE A 407 ARG A 413 1 7 HELIX 13 AB4 ASP A 423 LYS A 426 5 4 HELIX 14 AB5 TYR A 427 ILE A 439 1 13 HELIX 15 AB6 ILE A 439 ASN A 451 1 13 HELIX 16 AB7 ASN A 451 ASP A 461 1 11 HELIX 17 AB8 LYS A 484 GLU A 488 5 5 SHEET 1 AA1 7 MET A 128 ARG A 129 0 SHEET 2 AA1 7 HIS A 138 MET A 148 -1 O SER A 145 N MET A 128 SHEET 3 AA1 7 LEU A 400 VAL A 406 1 O LEU A 402 N HIS A 138 SHEET 4 AA1 7 SER A 187 PRO A 195 -1 N SER A 187 O VAL A 406 SHEET 5 AA1 7 THR A 344 GLY A 353 -1 O ILE A 349 N TYR A 192 SHEET 6 AA1 7 ILE A 325 VAL A 333 -1 N ASP A 330 O HIS A 352 SHEET 7 AA1 7 GLY A 306 ASN A 309 -1 N GLY A 306 O MET A 328 SHEET 1 AA2 7 ILE A 167 ARG A 174 0 SHEET 2 AA2 7 ARG A 75 TYR A 83 -1 N GLY A 82 O ARG A 168 SHEET 3 AA2 7 HIS A 138 MET A 148 -1 O ASN A 142 N VAL A 81 SHEET 4 AA2 7 LEU A 400 VAL A 406 1 O LEU A 402 N HIS A 138 SHEET 5 AA2 7 SER A 187 PRO A 195 -1 N SER A 187 O VAL A 406 SHEET 6 AA2 7 THR A 344 GLY A 353 -1 O ILE A 349 N TYR A 192 SHEET 7 AA2 7 PHE A 337 ILE A 339 -1 N PHE A 337 O TRP A 346 LINK O3' 5UD B 1 P A B 2 1555 1555 1.61 CISPEP 1 PRO A 95 PRO A 96 0 3.79 CRYST1 134.466 134.466 158.130 90.00 90.00 120.00 P 61 2 2 12 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 0.007437 0.004294 0.000000 0.00000 SCALE2 0.000000 0.008587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006324 0.00000