HEADER LIGASE 29-AUG-18 6HHV TITLE STRUCTURE OF T. THERMOPHILUS ASPRS IN COMPLEX WITH 5'-O-(N-(L- TITLE 2 ASPARTYL)-SULFAMOYL)N3-METHYLURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTATE--TRNA(ASP) LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ASPARTYL-TRNA SYNTHETASE; COMPND 5 SYNONYM: ASPARTYL-TRNA SYNTHETASE,ASPRS,DISCRIMINATING ASPARTYL-TRNA COMPND 6 SYNTHETASE,D-ASPRS; COMPND 7 EC: 6.1.1.12; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: ASPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS PROTEIN-INHIBITOR COMPLEX, TRNA AMINOACYLATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DE GRAEF,L.PANG,S.V.STRELKOV,S.D.WEEKS REVDAT 5 17-JAN-24 6HHV 1 REMARK REVDAT 4 04-MAR-20 6HHV 1 JRNL REVDAT 3 15-JAN-20 6HHV 1 JRNL REVDAT 2 08-JAN-20 6HHV 1 JRNL REVDAT 1 18-DEC-19 6HHV 0 JRNL AUTH L.PANG,M.NAUTIYAL,S.DE GRAEF,B.GADAKH,V.ZORZINI,A.ECONOMOU, JRNL AUTH 2 S.V.STRELKOV,A.VAN AERSCHOT,S.D.WEEKS JRNL TITL STRUCTURAL INSIGHTS INTO THE BINDING OF NATURAL JRNL TITL 2 PYRIMIDINE-BASED INHIBITORS OF CLASS II AMINOACYL-TRNA JRNL TITL 3 SYNTHETASES. JRNL REF ACS CHEM.BIOL. V. 15 407 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 31869198 JRNL DOI 10.1021/ACSCHEMBIO.9B00887 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 81376 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.550 REMARK 3 FREE R VALUE TEST SET COUNT : 2073 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 67.3146 - 5.3755 0.99 5408 115 0.1617 0.1739 REMARK 3 2 5.3755 - 4.2669 0.99 5312 143 0.1515 0.1658 REMARK 3 3 4.2669 - 3.7276 1.00 5283 146 0.1799 0.2235 REMARK 3 4 3.7276 - 3.3868 1.00 5290 132 0.1925 0.2355 REMARK 3 5 3.3868 - 3.1440 1.00 5278 143 0.2130 0.2493 REMARK 3 6 3.1440 - 2.9587 1.00 5245 161 0.2196 0.2586 REMARK 3 7 2.9587 - 2.8105 1.00 5296 139 0.2237 0.2781 REMARK 3 8 2.8105 - 2.6882 1.00 5258 160 0.2372 0.2822 REMARK 3 9 2.6882 - 2.5847 1.00 5293 126 0.2393 0.2808 REMARK 3 10 2.5847 - 2.4955 1.00 5270 135 0.2384 0.2847 REMARK 3 11 2.4955 - 2.4174 1.00 5269 137 0.2408 0.2833 REMARK 3 12 2.4174 - 2.3483 1.00 5263 133 0.2258 0.2544 REMARK 3 13 2.3483 - 2.2865 1.00 5262 139 0.2377 0.2984 REMARK 3 14 2.2865 - 2.2307 1.00 5308 123 0.2412 0.2812 REMARK 3 15 2.2307 - 2.1800 1.00 5268 141 0.2500 0.2748 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.15 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 0 THROUGH 578) REMARK 3 ORIGIN FOR THE GROUP (A): -27.0110 6.4401 -15.8622 REMARK 3 T TENSOR REMARK 3 T11: 0.3353 T22: 0.3180 REMARK 3 T33: 0.2794 T12: 0.0015 REMARK 3 T13: 0.0108 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.9095 L22: 0.7997 REMARK 3 L33: 0.6113 L12: -0.1254 REMARK 3 L13: -0.0117 L23: -0.1040 REMARK 3 S TENSOR REMARK 3 S11: -0.0132 S12: -0.1579 S13: 0.1615 REMARK 3 S21: 0.1495 S22: 0.1223 S23: -0.0591 REMARK 3 S31: -0.0491 S32: -0.0042 S33: -0.1041 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND NOT RESID 300:412) REMARK 3 ORIGIN FOR THE GROUP (A): -37.1305 -20.4178 -20.3452 REMARK 3 T TENSOR REMARK 3 T11: 0.4250 T22: 0.3363 REMARK 3 T33: 0.3518 T12: -0.0689 REMARK 3 T13: -0.0475 T23: 0.0547 REMARK 3 L TENSOR REMARK 3 L11: 0.8640 L22: 0.6308 REMARK 3 L33: 0.7574 L12: -0.2567 REMARK 3 L13: -0.2725 L23: 0.1632 REMARK 3 S TENSOR REMARK 3 S11: -0.0320 S12: -0.0212 S13: -0.1377 REMARK 3 S21: 0.0896 S22: 0.1228 S23: 0.0818 REMARK 3 S31: 0.1973 S32: -0.1200 S33: -0.0735 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 6HHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96863 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 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90892 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 67.283 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 REMARK 200 STARTING MODEL: 1L0W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A 10 MG/ML PROTEIN SOLUTION WAS REMARK 280 PREPARED IN 10 MM TRIS PH 7.5, 100 MM NACL, 2.5 MM DTT AND 0.4% REMARK 280 W/V LOW MELTING POINT AGAROSE, MAINTAINING THE SAMPLE REMARK 280 TEMPERATURE AT 315 KELVIN. CRYSTALS WERE GROWN BY MIXING AN REMARK 280 EQUAL VOLUME OF THE PROTEIN SOLUTION WITH 8-12% PEG 4000, 0.1 M REMARK 280 MORPHEUS BUFFER SYSTEM 1 (MES/IMIDAZOLE) PH 7, 100 MM KCL, 20 V/ REMARK 280 V % GLYCEROL. FOR SOAKING A 4 MM SOLUTION OF COMPOUND IN DMSO REMARK 280 WAS USED. A ONE THIRD VOLUME OF THE INITIAL DROP SIZE WAS REMARK 280 PIPETTED CAREFULLY ONTO THE CRYSTAL CONTAINING DROP. THE SAMPLE REMARK 280 WAS THEN PLACED BACK OVER THE RESERVOIR AND INCUBATED FOR REMARK 280 APPROXIMATELY 2 HR. CRYSTALS WE CAUGHT IN CRYOLOOPS AND DIRECTLY REMARK 280 FLASH FROZEN IN LIQUID NITROGEN., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 56.41300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 10780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 ASP A 432 REMARK 465 GLU A 433 REMARK 465 GLU A 434 REMARK 465 GLU A 435 REMARK 465 GLU A 436 REMARK 465 ARG A 579 REMARK 465 PRO A 580 REMARK 465 THR B 175 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 LYS A 120 CG CD CE NZ REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 ARG A 160 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 ARG A 228 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 231 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 LYS A 365 CG CD CE NZ REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 GLN A 376 CG CD OE1 NE2 REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 TRP A 431 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 431 CZ3 CH2 REMARK 470 GLU A 502 CG CD OE1 OE2 REMARK 470 ARG A 505 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 506 CG CD OE1 OE2 REMARK 470 GLU B 119 CG CD OE1 OE2 REMARK 470 LYS B 120 CG CD CE NZ REMARK 470 ASP B 226 CG OD1 OD2 REMARK 470 ARG B 228 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 300 CG CD CE NZ REMARK 470 ARG B 307 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 311 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 312 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 316 CG CD OE1 OE2 REMARK 470 GLU B 318 CG CD OE1 OE2 REMARK 470 LEU B 323 CG CD1 CD2 REMARK 470 LEU B 325 CG CD1 CD2 REMARK 470 LYS B 327 CG CD CE NZ REMARK 470 LEU B 329 CG CD1 CD2 REMARK 470 ARG B 331 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 332 CG CD CE NZ REMARK 470 GLU B 338 CG CD OE1 OE2 REMARK 470 GLU B 339 CG CD OE1 OE2 REMARK 470 LYS B 342 CG CD CE NZ REMARK 470 ARG B 343 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 345 CG CD CE NZ REMARK 470 GLN B 347 CG CD OE1 NE2 REMARK 470 LEU B 349 CG CD1 CD2 REMARK 470 ARG B 353 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 355 CG CD OE1 OE2 REMARK 470 GLU B 356 CG CD OE1 OE2 REMARK 470 LYS B 365 CG CD CE NZ REMARK 470 PHE B 366 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 368 CG CD OE1 OE2 REMARK 470 ARG B 371 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 372 CG CD OE1 OE2 REMARK 470 LEU B 374 CG CD1 CD2 REMARK 470 LEU B 375 CG CD1 CD2 REMARK 470 GLN B 376 CG CD OE1 NE2 REMARK 470 ARG B 381 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 393 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 394 CG CD CE NZ REMARK 470 LEU B 410 CG CD1 CD2 REMARK 470 LYS B 414 CG CD CE NZ REMARK 470 GLU B 433 CG CD OE1 OE2 REMARK 470 GLU B 434 CG CD OE1 OE2 REMARK 470 GLU B 435 CG CD OE1 OE2 REMARK 470 GLU B 502 CG CD OE1 OE2 REMARK 470 ARG B 505 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 506 CG CD OE1 OE2 REMARK 470 GLU B 567 CG CD OE1 OE2 REMARK 470 GLU B 568 CG CD OE1 OE2 REMARK 470 ARG B 579 CG CD NE CZ NH1 NH2 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 GLU A 66 -0.09 71.13 REMARK 500 ASP A 213 -49.04 70.83 REMARK 500 PRO A 304 7.90 -69.98 REMARK 500 LYS A 327 143.85 -173.60 REMARK 500 ALA A 352 148.80 -171.75 REMARK 500 LEU A 429 -169.99 -128.49 REMARK 500 GLU A 430 143.32 -171.50 REMARK 500 HIS A 442 -76.36 -103.06 REMARK 500 TYR B 130 54.58 -115.24 REMARK 500 ASP B 213 -47.69 67.70 REMARK 500 ASP B 226 97.88 -62.97 REMARK 500 LEU B 227 44.39 -66.09 REMARK 500 VAL B 370 77.46 -117.87 REMARK 500 GLU B 434 -73.36 -74.23 REMARK 500 ASP B 459 82.77 -155.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G5Q A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G5Q B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HHW RELATED DB: PDB REMARK 900 EC ASPRS IN COMPLEX WITH DSU REMARK 900 RELATED ID: 6HHX RELATED DB: PDB REMARK 900 EC ASPRS IN COMPLEX WITH DSC REMARK 900 RELATED ID: 6HI0 RELATED DB: PDB REMARK 900 RELATED ID: 6HHZ RELATED DB: PDB REMARK 900 RELATED ID: 6HHY RELATED DB: PDB REMARK 900 RELATED ID: 6HDZ RELATED DB: PDB REMARK 900 RELATED ID: 6HE3 RELATED DB: PDB REMARK 900 RELATED ID: 6HE1 RELATED DB: PDB DBREF 6HHV A 1 580 UNP P36419 SYD_THETH 1 580 DBREF 6HHV B 1 580 UNP P36419 SYD_THETH 1 580 SEQADV 6HHV GLY A 0 UNP P36419 EXPRESSION TAG SEQADV 6HHV GLY B 0 UNP P36419 EXPRESSION TAG SEQRES 1 A 581 GLY MET ARG ARG THR HIS TYR ALA GLY SER LEU ARG GLU SEQRES 2 A 581 THR HIS VAL GLY GLU GLU VAL VAL LEU GLU GLY TRP VAL SEQRES 3 A 581 ASN ARG ARG ARG ASP LEU GLY GLY LEU ILE PHE LEU ASP SEQRES 4 A 581 LEU ARG ASP ARG GLU GLY LEU VAL GLN LEU VAL ALA HIS SEQRES 5 A 581 PRO ALA SER PRO ALA TYR ALA THR ALA GLU ARG VAL ARG SEQRES 6 A 581 PRO GLU TRP VAL VAL ARG ALA LYS GLY LEU VAL ARG LEU SEQRES 7 A 581 ARG PRO GLU PRO ASN PRO ARG LEU ALA THR GLY ARG VAL SEQRES 8 A 581 GLU VAL GLU LEU SER ALA LEU GLU VAL LEU ALA GLU ALA SEQRES 9 A 581 LYS THR PRO PRO PHE PRO VAL ASP ALA GLY TRP ARG GLY SEQRES 10 A 581 GLU GLU GLU LYS GLU ALA SER GLU GLU LEU ARG LEU LYS SEQRES 11 A 581 TYR ARG TYR LEU ASP LEU ARG ARG ARG ARG MET GLN GLU SEQRES 12 A 581 ASN LEU ARG LEU ARG HIS ARG VAL ILE LYS ALA ILE TRP SEQRES 13 A 581 ASP PHE LEU ASP ARG GLU GLY PHE VAL GLN VAL GLU THR SEQRES 14 A 581 PRO PHE LEU THR LYS SER THR PRO GLU GLY ALA ARG ASP SEQRES 15 A 581 PHE LEU VAL PRO TYR ARG HIS GLU PRO GLY LEU PHE TYR SEQRES 16 A 581 ALA LEU PRO GLN SER PRO GLN LEU PHE LYS GLN MET LEU SEQRES 17 A 581 MET VAL ALA GLY LEU ASP ARG TYR PHE GLN ILE ALA ARG SEQRES 18 A 581 CYS PHE ARG ASP GLU ASP LEU ARG ALA ASP ARG GLN PRO SEQRES 19 A 581 ASP PHE THR GLN LEU ASP LEU GLU MET SER PHE VAL GLU SEQRES 20 A 581 VAL GLU ASP VAL LEU GLU LEU ASN GLU ARG LEU MET ALA SEQRES 21 A 581 HIS VAL PHE ARG GLU ALA LEU GLY VAL GLU LEU PRO LEU SEQRES 22 A 581 PRO PHE PRO ARG LEU SER TYR GLU GLU ALA MET GLU ARG SEQRES 23 A 581 TYR GLY SER ASP LYS PRO ASP LEU ARG PHE GLY LEU GLU SEQRES 24 A 581 LEU LYS GLU VAL GLY PRO LEU PHE ARG GLN SER GLY PHE SEQRES 25 A 581 ARG VAL PHE GLN GLU ALA GLU SER VAL LYS ALA LEU ALA SEQRES 26 A 581 LEU PRO LYS ALA LEU SER ARG LYS GLU VAL ALA GLU LEU SEQRES 27 A 581 GLU GLU VAL ALA LYS ARG HIS LYS ALA GLN GLY LEU ALA SEQRES 28 A 581 TRP ALA ARG VAL GLU GLU GLY GLY PHE SER GLY GLY VAL SEQRES 29 A 581 ALA LYS PHE LEU GLU PRO VAL ARG GLU ALA LEU LEU GLN SEQRES 30 A 581 ALA THR GLU ALA ARG PRO GLY ASP THR LEU LEU PHE VAL SEQRES 31 A 581 ALA GLY PRO ARG LYS VAL ALA ALA THR ALA LEU GLY ALA SEQRES 32 A 581 VAL ARG LEU ARG ALA ALA ASP LEU LEU GLY LEU LYS ARG SEQRES 33 A 581 GLU GLY PHE ARG PHE LEU TRP VAL VAL ASP PHE PRO LEU SEQRES 34 A 581 LEU GLU TRP ASP GLU GLU GLU GLU ALA TRP THR TYR MET SEQRES 35 A 581 HIS HIS PRO PHE THR SER PRO HIS PRO GLU ASP LEU PRO SEQRES 36 A 581 LEU LEU GLU LYS ASP PRO GLY ARG VAL ARG ALA LEU ALA SEQRES 37 A 581 TYR ASP LEU VAL LEU ASN GLY VAL GLU VAL GLY GLY GLY SEQRES 38 A 581 SER ILE ARG ILE HIS ASP PRO ARG LEU GLN ALA ARG VAL SEQRES 39 A 581 PHE ARG LEU LEU GLY ILE GLY GLU GLU GLU GLN ARG GLU SEQRES 40 A 581 LYS PHE GLY PHE PHE LEU GLU ALA LEU GLU TYR GLY ALA SEQRES 41 A 581 PRO PRO HIS GLY GLY ILE ALA TRP GLY LEU ASP ARG LEU SEQRES 42 A 581 LEU ALA LEU MET THR GLY SER PRO SER ILE ARG GLU VAL SEQRES 43 A 581 ILE ALA PHE PRO LYS ASN LYS GLU GLY LYS ASP PRO LEU SEQRES 44 A 581 THR GLY ALA PRO SER PRO VAL PRO GLU GLU GLN LEU ARG SEQRES 45 A 581 GLU LEU GLY LEU MET VAL VAL ARG PRO SEQRES 1 B 581 GLY MET ARG ARG THR HIS TYR ALA GLY SER LEU ARG GLU SEQRES 2 B 581 THR HIS VAL GLY GLU GLU VAL VAL LEU GLU GLY TRP VAL SEQRES 3 B 581 ASN ARG ARG ARG ASP LEU GLY GLY LEU ILE PHE LEU ASP SEQRES 4 B 581 LEU ARG ASP ARG GLU GLY LEU VAL GLN LEU VAL ALA HIS SEQRES 5 B 581 PRO ALA SER PRO ALA TYR ALA THR ALA GLU ARG VAL ARG SEQRES 6 B 581 PRO GLU TRP VAL VAL ARG ALA LYS GLY LEU VAL ARG LEU SEQRES 7 B 581 ARG PRO GLU PRO ASN PRO ARG LEU ALA THR GLY ARG VAL SEQRES 8 B 581 GLU VAL GLU LEU SER ALA LEU GLU VAL LEU ALA GLU ALA SEQRES 9 B 581 LYS THR PRO PRO PHE PRO VAL ASP ALA GLY TRP ARG GLY SEQRES 10 B 581 GLU GLU GLU LYS GLU ALA SER GLU GLU LEU ARG LEU LYS SEQRES 11 B 581 TYR ARG TYR LEU ASP LEU ARG ARG ARG ARG MET GLN GLU SEQRES 12 B 581 ASN LEU ARG LEU ARG HIS ARG VAL ILE LYS ALA ILE TRP SEQRES 13 B 581 ASP PHE LEU ASP ARG GLU GLY PHE VAL GLN VAL GLU THR SEQRES 14 B 581 PRO PHE LEU THR LYS SER THR PRO GLU GLY ALA ARG ASP SEQRES 15 B 581 PHE LEU VAL PRO TYR ARG HIS GLU PRO GLY LEU PHE TYR SEQRES 16 B 581 ALA LEU PRO GLN SER PRO GLN LEU PHE LYS GLN MET LEU SEQRES 17 B 581 MET VAL ALA GLY LEU ASP ARG TYR PHE GLN ILE ALA ARG SEQRES 18 B 581 CYS PHE ARG ASP GLU ASP LEU ARG ALA ASP ARG GLN PRO SEQRES 19 B 581 ASP PHE THR GLN LEU ASP LEU GLU MET SER PHE VAL GLU SEQRES 20 B 581 VAL GLU ASP VAL LEU GLU LEU ASN GLU ARG LEU MET ALA SEQRES 21 B 581 HIS VAL PHE ARG GLU ALA LEU GLY VAL GLU LEU PRO LEU SEQRES 22 B 581 PRO PHE PRO ARG LEU SER TYR GLU GLU ALA MET GLU ARG SEQRES 23 B 581 TYR GLY SER ASP LYS PRO ASP LEU ARG PHE GLY LEU GLU SEQRES 24 B 581 LEU LYS GLU VAL GLY PRO LEU PHE ARG GLN SER GLY PHE SEQRES 25 B 581 ARG VAL PHE GLN GLU ALA GLU SER VAL LYS ALA LEU ALA SEQRES 26 B 581 LEU PRO LYS ALA LEU SER ARG LYS GLU VAL ALA GLU LEU SEQRES 27 B 581 GLU GLU VAL ALA LYS ARG HIS LYS ALA GLN GLY LEU ALA SEQRES 28 B 581 TRP ALA ARG VAL GLU GLU GLY GLY PHE SER GLY GLY VAL SEQRES 29 B 581 ALA LYS PHE LEU GLU PRO VAL ARG GLU ALA LEU LEU GLN SEQRES 30 B 581 ALA THR GLU ALA ARG PRO GLY ASP THR LEU LEU PHE VAL SEQRES 31 B 581 ALA GLY PRO ARG LYS VAL ALA ALA THR ALA LEU GLY ALA SEQRES 32 B 581 VAL ARG LEU ARG ALA ALA ASP LEU LEU GLY LEU LYS ARG SEQRES 33 B 581 GLU GLY PHE ARG PHE LEU TRP VAL VAL ASP PHE PRO LEU SEQRES 34 B 581 LEU GLU TRP ASP GLU GLU GLU GLU ALA TRP THR TYR MET SEQRES 35 B 581 HIS HIS PRO PHE THR SER PRO HIS PRO GLU ASP LEU PRO SEQRES 36 B 581 LEU LEU GLU LYS ASP PRO GLY ARG VAL ARG ALA LEU ALA SEQRES 37 B 581 TYR ASP LEU VAL LEU ASN GLY VAL GLU VAL GLY GLY GLY SEQRES 38 B 581 SER ILE ARG ILE HIS ASP PRO ARG LEU GLN ALA ARG VAL SEQRES 39 B 581 PHE ARG LEU LEU GLY ILE GLY GLU GLU GLU GLN ARG GLU SEQRES 40 B 581 LYS PHE GLY PHE PHE LEU GLU ALA LEU GLU TYR GLY ALA SEQRES 41 B 581 PRO PRO HIS GLY GLY ILE ALA TRP GLY LEU ASP ARG LEU SEQRES 42 B 581 LEU ALA LEU MET THR GLY SER PRO SER ILE ARG GLU VAL SEQRES 43 B 581 ILE ALA PHE PRO LYS ASN LYS GLU GLY LYS ASP PRO LEU SEQRES 44 B 581 THR GLY ALA PRO SER PRO VAL PRO GLU GLU GLN LEU ARG SEQRES 45 B 581 GLU LEU GLY LEU MET VAL VAL ARG PRO HET G5Q A 601 30 HET G5Q B 601 30 HETNAM G5Q 5'-O-(N-(L-ASPARTYL)-SULFAMOYL)N3-METHYLURIDINE FORMUL 3 G5Q 2(C14 H20 N4 O11 S) FORMUL 5 HOH *161(H2 O) HELIX 1 AA1 TYR A 6 LEU A 10 5 5 HELIX 2 AA2 ARG A 11 VAL A 15 5 5 HELIX 3 AA3 ALA A 56 VAL A 63 1 8 HELIX 4 AA4 ALA A 112 GLY A 116 5 5 HELIX 5 AA5 SER A 123 TYR A 130 1 8 HELIX 6 AA6 TYR A 130 LEU A 135 1 6 HELIX 7 AA7 ARG A 137 GLU A 161 1 25 HELIX 8 AA8 PRO A 200 ALA A 210 1 11 HELIX 9 AA9 GLU A 246 GLY A 267 1 22 HELIX 10 AB1 TYR A 279 GLY A 287 1 9 HELIX 11 AB2 GLY A 303 PHE A 306 5 4 HELIX 12 AB3 PHE A 311 ALA A 317 1 7 HELIX 13 AB4 SER A 330 ARG A 343 1 14 HELIX 14 AB5 VAL A 363 GLU A 368 1 6 HELIX 15 AB6 VAL A 370 GLU A 379 1 10 HELIX 16 AB7 PRO A 392 LEU A 411 1 20 HELIX 17 AB8 HIS A 449 LEU A 453 5 5 HELIX 18 AB9 PRO A 454 ASP A 459 1 6 HELIX 19 AC1 PRO A 460 VAL A 463 5 4 HELIX 20 AC2 ASP A 486 GLY A 498 1 13 HELIX 21 AC3 GLY A 500 LEU A 515 1 16 HELIX 22 AC4 GLU A 516 GLY A 518 5 3 HELIX 23 AC5 LEU A 529 THR A 537 1 9 HELIX 24 AC6 SER A 541 ILE A 546 5 6 HELIX 25 AC7 PRO A 566 GLU A 572 1 7 HELIX 26 AC8 TYR B 6 LEU B 10 5 5 HELIX 27 AC9 ARG B 11 VAL B 15 5 5 HELIX 28 AD1 ALA B 56 VAL B 63 1 8 HELIX 29 AD2 ALA B 112 GLY B 116 5 5 HELIX 30 AD3 SER B 123 TYR B 130 1 8 HELIX 31 AD4 TYR B 130 LEU B 135 1 6 HELIX 32 AD5 ARG B 137 GLU B 161 1 25 HELIX 33 AD6 PRO B 200 ALA B 210 1 11 HELIX 34 AD7 GLU B 246 GLY B 267 1 22 HELIX 35 AD8 TYR B 279 GLY B 287 1 9 HELIX 36 AD9 GLY B 303 PHE B 306 5 4 HELIX 37 AE1 PHE B 311 GLU B 316 1 6 HELIX 38 AE2 SER B 330 HIS B 344 1 15 HELIX 39 AE3 VAL B 363 GLU B 368 1 6 HELIX 40 AE4 ARG B 371 GLU B 379 1 9 HELIX 41 AE5 PRO B 392 LEU B 411 1 20 HELIX 42 AE6 HIS B 449 LEU B 453 5 5 HELIX 43 AE7 PRO B 454 ASP B 459 1 6 HELIX 44 AE8 PRO B 460 VAL B 463 5 4 HELIX 45 AE9 ASP B 486 LEU B 497 1 12 HELIX 46 AF1 GLY B 500 LEU B 515 1 16 HELIX 47 AF2 GLU B 516 GLY B 518 5 3 HELIX 48 AF3 LEU B 529 THR B 537 1 9 HELIX 49 AF4 SER B 541 ILE B 546 5 6 HELIX 50 AF5 PRO B 566 LEU B 573 1 8 SHEET 1 AA1 6 GLU A 18 LEU A 31 0 SHEET 2 AA1 6 LEU A 34 ASP A 41 -1 O PHE A 36 N ARG A 29 SHEET 3 AA1 6 GLY A 44 ALA A 50 -1 O LEU A 48 N LEU A 37 SHEET 4 AA1 6 VAL A 90 ALA A 101 1 O LEU A 94 N VAL A 49 SHEET 5 AA1 6 VAL A 68 LEU A 77 -1 N ARG A 76 O GLU A 91 SHEET 6 AA1 6 GLU A 18 LEU A 31 -1 N LEU A 21 O ALA A 71 SHEET 1 AA2 8 VAL A 164 GLN A 165 0 SHEET 2 AA2 8 ARG A 214 PHE A 222 1 O ARG A 214 N VAL A 164 SHEET 3 AA2 8 ASP A 234 SER A 243 -1 O GLN A 237 N ALA A 219 SHEET 4 AA2 8 HIS A 522 GLY A 528 -1 O GLY A 523 N MET A 242 SHEET 5 AA2 8 VAL A 475 ILE A 482 -1 N VAL A 477 O GLY A 528 SHEET 6 AA2 8 ALA A 467 LEU A 472 -1 N LEU A 472 O VAL A 475 SHEET 7 AA2 8 PHE A 420 VAL A 424 -1 N LEU A 421 O VAL A 471 SHEET 8 AA2 8 ARG A 276 SER A 278 1 N LEU A 277 O VAL A 424 SHEET 1 AA3 2 LEU A 183 PRO A 185 0 SHEET 2 AA3 2 PHE A 193 ALA A 195 -1 O TYR A 194 N VAL A 184 SHEET 1 AA4 5 LYS A 300 GLU A 301 0 SHEET 2 AA4 5 SER A 319 LEU A 325 -1 O ALA A 322 N LYS A 300 SHEET 3 AA4 5 THR A 385 GLY A 391 -1 O LEU A 387 N LEU A 323 SHEET 4 AA4 5 ALA A 350 VAL A 354 -1 N ALA A 352 O LEU A 386 SHEET 5 AA4 5 PHE A 359 SER A 360 -1 O SER A 360 N ARG A 353 SHEET 1 AA5 2 LEU A 429 GLU A 430 0 SHEET 2 AA5 2 THR A 439 TYR A 440 -1 O THR A 439 N GLU A 430 SHEET 1 AA6 2 LEU A 575 VAL A 577 0 SHEET 2 AA6 2 LEU B 575 VAL B 577 -1 O MET B 576 N MET A 576 SHEET 1 AA7 6 GLU B 18 LEU B 31 0 SHEET 2 AA7 6 LEU B 34 ASP B 41 -1 O ASP B 38 N ASN B 26 SHEET 3 AA7 6 GLY B 44 ALA B 50 -1 O LEU B 48 N LEU B 37 SHEET 4 AA7 6 VAL B 90 ALA B 101 1 O LEU B 94 N VAL B 49 SHEET 5 AA7 6 VAL B 68 LEU B 77 -1 N LYS B 72 O SER B 95 SHEET 6 AA7 6 GLU B 18 LEU B 31 -1 N LEU B 21 O ALA B 71 SHEET 1 AA8 8 VAL B 164 GLN B 165 0 SHEET 2 AA8 8 ARG B 214 PHE B 222 1 O ARG B 214 N VAL B 164 SHEET 3 AA8 8 ASP B 234 SER B 243 -1 O ASP B 239 N GLN B 217 SHEET 4 AA8 8 HIS B 522 GLY B 528 -1 O GLY B 523 N MET B 242 SHEET 5 AA8 8 VAL B 475 ILE B 482 -1 N VAL B 477 O GLY B 528 SHEET 6 AA8 8 ALA B 467 LEU B 472 -1 N LEU B 472 O VAL B 475 SHEET 7 AA8 8 PHE B 420 VAL B 424 -1 N LEU B 421 O VAL B 471 SHEET 8 AA8 8 ARG B 276 SER B 278 1 N LEU B 277 O TRP B 422 SHEET 1 AA9 2 LEU B 183 PRO B 185 0 SHEET 2 AA9 2 PHE B 193 ALA B 195 -1 O TYR B 194 N VAL B 184 SHEET 1 AB1 4 LYS B 300 GLU B 301 0 SHEET 2 AB1 4 SER B 319 LEU B 325 -1 O ALA B 322 N LYS B 300 SHEET 3 AB1 4 THR B 385 GLY B 391 -1 O GLY B 391 N SER B 319 SHEET 4 AB1 4 ALA B 350 TRP B 351 -1 N ALA B 350 O PHE B 388 SHEET 1 AB2 2 ARG B 353 VAL B 354 0 SHEET 2 AB2 2 PHE B 359 SER B 360 -1 O SER B 360 N ARG B 353 SHEET 1 AB3 2 LEU B 429 ASP B 432 0 SHEET 2 AB3 2 ALA B 437 TYR B 440 -1 O THR B 439 N GLU B 430 CISPEP 1 LEU A 272 PRO A 273 0 2.29 CISPEP 2 ALA A 561 PRO A 562 0 -2.91 CISPEP 3 LEU B 272 PRO B 273 0 -0.67 CISPEP 4 ALA B 561 PRO B 562 0 -7.01 SITE 1 AC1 20 SER A 199 GLN A 201 LYS A 204 ARG A 223 SITE 2 AC1 20 PHE A 235 GLN A 237 HIS A 442 HIS A 443 SITE 3 AC1 20 GLU A 476 VAL A 477 GLY A 478 GLY A 479 SITE 4 AC1 20 GLY A 480 ARG A 483 ILE A 525 ALA A 526 SITE 5 AC1 20 GLY A 528 ARG A 531 HOH A 729 HOH A 734 SITE 1 AC2 20 GLU B 177 SER B 199 GLN B 201 LYS B 204 SITE 2 AC2 20 ARG B 223 PHE B 235 GLN B 237 HIS B 443 SITE 3 AC2 20 GLU B 476 VAL B 477 GLY B 478 GLY B 479 SITE 4 AC2 20 GLY B 480 ARG B 483 ILE B 525 ALA B 526 SITE 5 AC2 20 GLY B 528 ARG B 531 HOH B 710 HOH B 712 CRYST1 82.218 112.826 88.533 90.00 104.38 90.00 P 1 21 1 4 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 0.012163 0.000000 0.003119 0.00000 SCALE2 0.000000 0.008863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011661 0.00000