HEADER LIGASE 09-AUG-18 6HB7 TITLE CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L-TYROSYL) TITLE 2 SULFAMOYL-N3-METHYLURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYROSYL-TRNA SYNTHETASE,TYRRS; COMPND 5 EC: 6.1.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 GENE: TYRS, ECBD_2006; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS PROTEIN-INHIBITOR COMPLEX, ROSSMANN FOLD, TRNA AMINOACYLATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DE GRAEF,L.PANG,S.V.STRELKOV,S.D.WEEKS REVDAT 3 01-MAY-19 6HB7 1 REMARK REVDAT 2 24-APR-19 6HB7 1 JRNL REVDAT 1 17-APR-19 6HB7 0 JRNL AUTH M.NAUTIYAL,S.DE GRAEF,L.PANG,B.GADAKH,S.V.STRELKOV, JRNL AUTH 2 S.D.WEEKS,A.VAN AERSCHOT JRNL TITL COMPARATIVE ANALYSIS OF PYRIMIDINE SUBSTITUTED JRNL TITL 2 AMINOACYL-SULFAMOYL NUCLEOSIDES AS POTENTIAL INHIBITORS JRNL TITL 3 TARGETING CLASS I AMINOACYL-TRNA SYNTHETASES. JRNL REF EUR.J.MED.CHEM. V. 173 154 2019 JRNL REFN ISSN 0223-5234 JRNL PMID 30995568 JRNL DOI 10.1016/J.EJMECH.2019.04.003 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 71119 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2129 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.87 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 5257 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2656 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5094 REMARK 3 BIN R VALUE (WORKING SET) : 0.2641 REMARK 3 BIN FREE R VALUE : 0.3164 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6387 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 608 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.14480 REMARK 3 B22 (A**2) : -3.65940 REMARK 3 B33 (A**2) : -3.48540 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 8.83520 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.230 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.160 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.142 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.155 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.141 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6616 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8966 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2291 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 190 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 995 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6616 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 854 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 8216 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.01 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.10 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.27 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { B|4 - B|243 } REMARK 3 ORIGIN FOR THE GROUP (A): -38.8458 2.0275 -8.8533 REMARK 3 T TENSOR REMARK 3 T11: 0.2124 T22: 0.2151 REMARK 3 T33: 0.1823 T12: -0.0136 REMARK 3 T13: 0.0186 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.1970 L22: 0.8991 REMARK 3 L33: 2.9368 L12: -0.2439 REMARK 3 L13: 1.8951 L23: -0.3795 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: -0.2667 S13: -0.0913 REMARK 3 S21: 0.0760 S22: 0.0347 S23: 0.0914 REMARK 3 S31: -0.0186 S32: -0.2514 S33: -0.0891 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|244 - B|329 } REMARK 3 ORIGIN FOR THE GROUP (A): -16.9370 7.8160 8.0461 REMARK 3 T TENSOR REMARK 3 T11: 0.2653 T22: 0.3116 REMARK 3 T33: 0.1838 T12: -0.0801 REMARK 3 T13: -0.0487 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 1.8735 L22: 3.0067 REMARK 3 L33: 4.4181 L12: -0.8093 REMARK 3 L13: 0.4791 L23: 1.0597 REMARK 3 S TENSOR REMARK 3 S11: -0.2034 S12: 0.1049 S13: 0.1091 REMARK 3 S21: 0.2297 S22: 0.1348 S23: -0.3508 REMARK 3 S31: -0.3413 S32: 0.4499 S33: 0.0686 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|330 - B|424 } REMARK 3 ORIGIN FOR THE GROUP (A): 8.6776 5.0135 -4.5921 REMARK 3 T TENSOR REMARK 3 T11: 0.3436 T22: 0.5732 REMARK 3 T33: 0.6319 T12: 0.0872 REMARK 3 T13: 0.0528 T23: -0.2398 REMARK 3 L TENSOR REMARK 3 L11: 7.5516 L22: 0.6709 REMARK 3 L33: 2.8270 L12: 0.7074 REMARK 3 L13: -0.8063 L23: -0.3946 REMARK 3 S TENSOR REMARK 3 S11: 0.1580 S12: 0.1634 S13: 0.0711 REMARK 3 S21: -0.1736 S22: 0.1549 S23: -0.3271 REMARK 3 S31: 0.1697 S32: 0.4402 S33: -0.3130 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|5 - A|235 } REMARK 3 ORIGIN FOR THE GROUP (A): -48.9094 1.5050 -44.9118 REMARK 3 T TENSOR REMARK 3 T11: 0.1302 T22: 0.1258 REMARK 3 T33: 0.1467 T12: 0.0023 REMARK 3 T13: 0.0266 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.3725 L22: 1.1178 REMARK 3 L33: 0.8800 L12: 0.1013 REMARK 3 L13: 0.3053 L23: -0.2850 REMARK 3 S TENSOR REMARK 3 S11: -0.0130 S12: 0.1754 S13: 0.0238 REMARK 3 S21: -0.0167 S22: 0.0359 S23: -0.0176 REMARK 3 S31: 0.0038 S32: -0.0233 S33: -0.0229 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { A|236 - A|264 } REMARK 3 ORIGIN FOR THE GROUP (A): -72.6783 4.9684 -53.8423 REMARK 3 T TENSOR REMARK 3 T11: 0.1294 T22: 0.1631 REMARK 3 T33: 0.1673 T12: 0.0208 REMARK 3 T13: 0.0166 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 4.3523 L22: 3.9788 REMARK 3 L33: 1.6830 L12: 1.3365 REMARK 3 L13: 0.8694 L23: -2.0053 REMARK 3 S TENSOR REMARK 3 S11: -0.1559 S12: 0.2350 S13: 0.3064 REMARK 3 S21: 0.1533 S22: -0.0273 S23: 0.0137 REMARK 3 S31: -0.2252 S32: -0.0676 S33: 0.1833 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { A|265 - A|424 } REMARK 3 ORIGIN FOR THE GROUP (A): -86.5469 5.0187 -57.3615 REMARK 3 T TENSOR REMARK 3 T11: 0.1479 T22: 0.1584 REMARK 3 T33: 0.1486 T12: -0.0158 REMARK 3 T13: 0.0359 T23: 0.0412 REMARK 3 L TENSOR REMARK 3 L11: 2.5369 L22: 0.2347 REMARK 3 L33: 0.5436 L12: -0.0022 REMARK 3 L13: 0.0343 L23: -0.1691 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: 0.2723 S13: 0.0918 REMARK 3 S21: 0.0409 S22: -0.0238 S23: 0.0553 REMARK 3 S31: -0.0431 S32: 0.0938 S33: 0.0571 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200010913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : SI(111) 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 : 76335 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 88.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.77700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HOLO ENZYME CRYSTALS WERE GROWN IN 0.1 REMARK 280 M BIS-TRIS PH 6.5, 10-15% PEG 3350, 20 MM GLUTAMATE (1M STOCK REMARK 280 SOLUTION ADJUSTED TO PH 6), 20% (V/V) ETHYLENE GLYCOL FOR REMARK 280 SOAKING CRYSTALS WERE TRANSFERRED TO DROP CONTAINING MOTHER REMARK 280 LIQUOR SUPPLEMENTED WITH 2 MM INHIBITOR., VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 32.30650 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 THR A 239 REMARK 465 GLU A 240 REMARK 465 GLY A 241 REMARK 465 GLY A 242 REMARK 465 SER A 293 REMARK 465 GLY A 294 REMARK 465 LYS A 295 REMARK 465 ALA A 296 REMARK 465 PRO A 297 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 LYS B 235 REMARK 465 PHE B 236 REMARK 465 GLY B 237 REMARK 465 LYS B 238 REMARK 465 THR B 239 REMARK 465 GLU B 240 REMARK 465 GLY B 241 REMARK 465 GLY B 242 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 8 CG CD CE NZ REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 GLU A 118 CG CD OE1 OE2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 ASP A 290 CG OD1 OD2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 LYS A 415 CG CD CE NZ REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 ARG B 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 GLU B 118 CG CD OE1 OE2 REMARK 470 GLU B 155 CG CD OE1 OE2 REMARK 470 ARG B 163 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 164 CG CD OE1 OE2 REMARK 470 ASP B 165 CG OD1 OD2 REMARK 470 THR B 234 OG1 CG2 REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 PHE B 328 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 354 CG CD OE1 OE2 REMARK 470 ARG B 372 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 377 CG CD CE NZ REMARK 470 LYS B 390 CG CD CE NZ REMARK 470 GLU B 395 CG CD OE1 OE2 REMARK 470 PHE B 398 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 399 CG CD CE NZ REMARK 470 GLU B 400 CG CD OE1 OE2 REMARK 470 LYS B 415 CG CD CE NZ REMARK 470 LYS B 416 CG CD CE NZ REMARK 470 LYS B 424 CG CD CE NZ 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 ASP A 21 50.97 33.77 REMARK 500 CYS A 116 34.07 -140.61 REMARK 500 ASP A 346 2.21 -160.21 REMARK 500 SER B 83 108.19 -47.58 REMARK 500 ASP B 346 -3.02 -161.03 REMARK 500 PHE B 397 -66.43 -97.04 REMARK 500 PHE B 398 120.15 140.32 REMARK 500 ARG B 407 -8.44 -151.04 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 Y3U A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Y3U B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HB6 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH YSU REMARK 900 RELATED ID: 6HB5 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH YSC DBREF1 6HB7 A 1 424 UNP A0A140NBN7_ECOBD DBREF2 6HB7 A A0A140NBN7 1 424 DBREF1 6HB7 B 1 424 UNP A0A140NBN7_ECOBD DBREF2 6HB7 B A0A140NBN7 1 424 SEQRES 1 A 424 MET ALA SER SER ASN LEU ILE LYS GLN LEU GLN GLU ARG SEQRES 2 A 424 GLY LEU VAL ALA GLN VAL THR ASP GLU GLU ALA LEU ALA SEQRES 3 A 424 GLU ARG LEU ALA GLN GLY PRO ILE ALA LEU TYR CYS GLY SEQRES 4 A 424 PHE ASP PRO THR ALA ASP SER LEU HIS LEU GLY HIS LEU SEQRES 5 A 424 VAL PRO LEU LEU CYS LEU LYS ARG PHE GLN GLN ALA GLY SEQRES 6 A 424 HIS LYS PRO VAL ALA LEU VAL GLY GLY ALA THR GLY LEU SEQRES 7 A 424 ILE GLY ASP PRO SER PHE LYS ALA ALA GLU ARG LYS LEU SEQRES 8 A 424 ASN THR GLU GLU THR VAL GLN GLU TRP VAL ASP LYS ILE SEQRES 9 A 424 ARG LYS GLN VAL ALA PRO PHE LEU ASP PHE ASP CYS GLY SEQRES 10 A 424 GLU ASN SER ALA ILE ALA ALA ASN ASN TYR ASP TRP PHE SEQRES 11 A 424 GLY ASN MET ASN VAL LEU THR PHE LEU ARG ASP ILE GLY SEQRES 12 A 424 LYS HIS PHE SER VAL ASN GLN MET ILE ASN LYS GLU ALA SEQRES 13 A 424 VAL LYS GLN ARG LEU ASN ARG GLU ASP GLN GLY ILE SER SEQRES 14 A 424 PHE THR GLU PHE SER TYR ASN LEU LEU GLN GLY TYR ASP SEQRES 15 A 424 PHE ALA CYS LEU ASN LYS GLN TYR GLY VAL VAL LEU GLN SEQRES 16 A 424 ILE GLY GLY SER ASP GLN TRP GLY ASN ILE THR SER GLY SEQRES 17 A 424 ILE ASP LEU THR ARG ARG LEU HIS GLN ASN GLN VAL PHE SEQRES 18 A 424 GLY LEU THR VAL PRO LEU ILE THR LYS ALA ASP GLY THR SEQRES 19 A 424 LYS PHE GLY LYS THR GLU GLY GLY ALA VAL TRP LEU ASP SEQRES 20 A 424 PRO LYS LYS THR SER PRO TYR LYS PHE TYR GLN PHE TRP SEQRES 21 A 424 ILE ASN THR ALA ASP ALA ASP VAL TYR ARG PHE LEU LYS SEQRES 22 A 424 PHE PHE THR PHE MET SER ILE GLU GLU ILE ASN ALA LEU SEQRES 23 A 424 GLU GLU GLU ASP LYS ASN SER GLY LYS ALA PRO ARG ALA SEQRES 24 A 424 GLN TYR VAL LEU ALA GLU GLN VAL THR ARG LEU VAL HIS SEQRES 25 A 424 GLY GLU GLU GLY LEU GLN ALA ALA LYS ARG ILE THR GLU SEQRES 26 A 424 CYS LEU PHE SER GLY SER LEU SER ALA LEU SER GLU ALA SEQRES 27 A 424 ASP PHE GLU GLN LEU ALA GLN ASP GLY VAL PRO MET VAL SEQRES 28 A 424 GLU MET GLU LYS GLY ALA ASP LEU MET GLN ALA LEU VAL SEQRES 29 A 424 ASP SER GLU LEU GLN PRO SER ARG GLY GLN ALA ARG LYS SEQRES 30 A 424 THR ILE ALA SER ASN ALA ILE THR ILE ASN GLY GLU LYS SEQRES 31 A 424 GLN SER ASP PRO GLU TYR PHE PHE LYS GLU GLU GLU ARG SEQRES 32 A 424 LEU PHE GLY ARG PHE THR LEU LEU ARG ARG GLY LYS LYS SEQRES 33 A 424 ASN TYR CYS LEU ILE CYS TRP LYS SEQRES 1 B 424 MET ALA SER SER ASN LEU ILE LYS GLN LEU GLN GLU ARG SEQRES 2 B 424 GLY LEU VAL ALA GLN VAL THR ASP GLU GLU ALA LEU ALA SEQRES 3 B 424 GLU ARG LEU ALA GLN GLY PRO ILE ALA LEU TYR CYS GLY SEQRES 4 B 424 PHE ASP PRO THR ALA ASP SER LEU HIS LEU GLY HIS LEU SEQRES 5 B 424 VAL PRO LEU LEU CYS LEU LYS ARG PHE GLN GLN ALA GLY SEQRES 6 B 424 HIS LYS PRO VAL ALA LEU VAL GLY GLY ALA THR GLY LEU SEQRES 7 B 424 ILE GLY ASP PRO SER PHE LYS ALA ALA GLU ARG LYS LEU SEQRES 8 B 424 ASN THR GLU GLU THR VAL GLN GLU TRP VAL ASP LYS ILE SEQRES 9 B 424 ARG LYS GLN VAL ALA PRO PHE LEU ASP PHE ASP CYS GLY SEQRES 10 B 424 GLU ASN SER ALA ILE ALA ALA ASN ASN TYR ASP TRP PHE SEQRES 11 B 424 GLY ASN MET ASN VAL LEU THR PHE LEU ARG ASP ILE GLY SEQRES 12 B 424 LYS HIS PHE SER VAL ASN GLN MET ILE ASN LYS GLU ALA SEQRES 13 B 424 VAL LYS GLN ARG LEU ASN ARG GLU ASP GLN GLY ILE SER SEQRES 14 B 424 PHE THR GLU PHE SER TYR ASN LEU LEU GLN GLY TYR ASP SEQRES 15 B 424 PHE ALA CYS LEU ASN LYS GLN TYR GLY VAL VAL LEU GLN SEQRES 16 B 424 ILE GLY GLY SER ASP GLN TRP GLY ASN ILE THR SER GLY SEQRES 17 B 424 ILE ASP LEU THR ARG ARG LEU HIS GLN ASN GLN VAL PHE SEQRES 18 B 424 GLY LEU THR VAL PRO LEU ILE THR LYS ALA ASP GLY THR SEQRES 19 B 424 LYS PHE GLY LYS THR GLU GLY GLY ALA VAL TRP LEU ASP SEQRES 20 B 424 PRO LYS LYS THR SER PRO TYR LYS PHE TYR GLN PHE TRP SEQRES 21 B 424 ILE ASN THR ALA ASP ALA ASP VAL TYR ARG PHE LEU LYS SEQRES 22 B 424 PHE PHE THR PHE MET SER ILE GLU GLU ILE ASN ALA LEU SEQRES 23 B 424 GLU GLU GLU ASP LYS ASN SER GLY LYS ALA PRO ARG ALA SEQRES 24 B 424 GLN TYR VAL LEU ALA GLU GLN VAL THR ARG LEU VAL HIS SEQRES 25 B 424 GLY GLU GLU GLY LEU GLN ALA ALA LYS ARG ILE THR GLU SEQRES 26 B 424 CYS LEU PHE SER GLY SER LEU SER ALA LEU SER GLU ALA SEQRES 27 B 424 ASP PHE GLU GLN LEU ALA GLN ASP GLY VAL PRO MET VAL SEQRES 28 B 424 GLU MET GLU LYS GLY ALA ASP LEU MET GLN ALA LEU VAL SEQRES 29 B 424 ASP SER GLU LEU GLN PRO SER ARG GLY GLN ALA ARG LYS SEQRES 30 B 424 THR ILE ALA SER ASN ALA ILE THR ILE ASN GLY GLU LYS SEQRES 31 B 424 GLN SER ASP PRO GLU TYR PHE PHE LYS GLU GLU GLU ARG SEQRES 32 B 424 LEU PHE GLY ARG PHE THR LEU LEU ARG ARG GLY LYS LYS SEQRES 33 B 424 ASN TYR CYS LEU ILE CYS TRP LYS HET Y3U A 501 34 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET CL A 505 1 HET Y3U B 501 34 HETNAM Y3U [(2~{R},3~{S},4~{R},5~{R})-5-[3-METHYL-2,4- HETNAM 2 Y3U BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3,4-BIS(OXIDANYL) HETNAM 3 Y3U OXOLAN-2-YL]METHYL ~{N}-[(2~{S})-2-AZANYL-3-(4- HETNAM 4 Y3U HYDROXYPHENYL)PROPANOYL]SULFAMATE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 Y3U 2(C19 H24 N4 O10 S) FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 CL CL 1- FORMUL 9 HOH *608(H2 O) HELIX 1 AA1 ASN A 5 ARG A 13 1 9 HELIX 2 AA2 ASP A 21 GLY A 32 1 12 HELIX 3 AA3 HIS A 48 ALA A 64 1 17 HELIX 4 AA4 ALA A 75 ILE A 79 5 5 HELIX 5 AA5 THR A 93 ALA A 109 1 17 HELIX 6 AA6 PRO A 110 LEU A 112 5 3 HELIX 7 AA7 CYS A 116 SER A 120 5 5 HELIX 8 AA8 ASN A 126 GLY A 131 1 6 HELIX 9 AA9 ASN A 134 ILE A 142 1 9 HELIX 10 AB1 GLY A 143 PHE A 146 5 4 HELIX 11 AB2 SER A 147 ILE A 152 1 6 HELIX 12 AB3 LYS A 154 GLN A 159 1 6 HELIX 13 AB4 ARG A 163 GLY A 167 5 5 HELIX 14 AB5 SER A 169 SER A 174 1 6 HELIX 15 AB6 SER A 174 GLY A 191 1 18 HELIX 16 AB7 GLN A 201 GLN A 217 1 17 HELIX 17 AB8 SER A 252 ASN A 262 1 11 HELIX 18 AB9 ALA A 264 THR A 276 1 13 HELIX 19 AC1 SER A 279 ASN A 292 1 14 HELIX 20 AC2 ALA A 299 GLY A 330 1 32 HELIX 21 AC3 SER A 336 GLY A 347 1 12 HELIX 22 AC4 ASP A 358 SER A 366 1 9 HELIX 23 AC5 SER A 371 SER A 381 1 11 HELIX 24 AC6 LYS A 399 GLY A 406 5 8 HELIX 25 AC7 ASN B 5 ARG B 13 1 9 HELIX 26 AC8 ASP B 21 GLY B 32 1 12 HELIX 27 AC9 HIS B 48 ALA B 64 1 17 HELIX 28 AD1 ALA B 75 ILE B 79 5 5 HELIX 29 AD2 THR B 93 ALA B 109 1 17 HELIX 30 AD3 PRO B 110 LEU B 112 5 3 HELIX 31 AD4 ASN B 126 GLY B 131 1 6 HELIX 32 AD5 ASN B 134 ILE B 142 1 9 HELIX 33 AD6 GLY B 143 PHE B 146 5 4 HELIX 34 AD7 SER B 147 ASN B 153 1 7 HELIX 35 AD8 LYS B 154 GLN B 159 1 6 HELIX 36 AD9 ARG B 160 ASN B 162 5 3 HELIX 37 AE1 ARG B 163 GLY B 167 5 5 HELIX 38 AE2 SER B 169 GLY B 191 1 23 HELIX 39 AE3 GLN B 201 GLN B 217 1 17 HELIX 40 AE4 SER B 252 ASN B 262 1 11 HELIX 41 AE5 ALA B 264 THR B 276 1 13 HELIX 42 AE6 SER B 279 SER B 293 1 15 HELIX 43 AE7 ARG B 298 GLY B 330 1 33 HELIX 44 AE8 SER B 336 ASP B 346 1 11 HELIX 45 AE9 ASP B 358 SER B 366 1 9 HELIX 46 AF1 SER B 371 SER B 381 1 11 HELIX 47 AF2 LYS B 399 GLY B 406 5 8 SHEET 1 AA1 6 GLN A 18 VAL A 19 0 SHEET 2 AA1 6 PHE A 221 VAL A 225 -1 O THR A 224 N GLN A 18 SHEET 3 AA1 6 VAL A 192 GLY A 198 1 N VAL A 193 O PHE A 221 SHEET 4 AA1 6 ALA A 35 PHE A 40 1 N ALA A 35 O VAL A 193 SHEET 5 AA1 6 LYS A 67 VAL A 72 1 O LYS A 67 N LEU A 36 SHEET 6 AA1 6 ILE A 122 ASN A 125 1 O ALA A 124 N VAL A 72 SHEET 1 AA2 5 MET A 350 MET A 353 0 SHEET 2 AA2 5 ASN A 417 TRP A 423 1 O CYS A 422 N VAL A 351 SHEET 3 AA2 5 PHE A 408 ARG A 413 -1 N THR A 409 O ILE A 421 SHEET 4 AA2 5 ILE A 384 ILE A 386 -1 N THR A 385 O ARG A 412 SHEET 5 AA2 5 GLU A 389 LYS A 390 -1 O GLU A 389 N ILE A 386 SHEET 1 AA3 6 GLN B 18 VAL B 19 0 SHEET 2 AA3 6 PHE B 221 VAL B 225 -1 O THR B 224 N GLN B 18 SHEET 3 AA3 6 VAL B 192 GLY B 198 1 N VAL B 193 O PHE B 221 SHEET 4 AA3 6 ALA B 35 PHE B 40 1 N TYR B 37 O ILE B 196 SHEET 5 AA3 6 LYS B 67 VAL B 72 1 O LEU B 71 N CYS B 38 SHEET 6 AA3 6 ILE B 122 ASN B 125 1 O ILE B 122 N ALA B 70 SHEET 1 AA4 5 MET B 350 GLU B 354 0 SHEET 2 AA4 5 ASN B 417 LYS B 424 1 O CYS B 422 N VAL B 351 SHEET 3 AA4 5 PHE B 408 ARG B 413 -1 N THR B 409 O ILE B 421 SHEET 4 AA4 5 ILE B 384 ILE B 386 -1 N THR B 385 O ARG B 412 SHEET 5 AA4 5 GLU B 389 LYS B 390 -1 O GLU B 389 N ILE B 386 SITE 1 AC1 25 TYR A 37 GLY A 39 ASP A 41 GLY A 50 SITE 2 AC1 25 HIS A 51 PRO A 54 LEU A 71 THR A 76 SITE 3 AC1 25 ASP A 81 TYR A 175 GLN A 179 ASP A 182 SITE 4 AC1 25 GLN A 195 GLY A 197 GLY A 198 ASP A 200 SITE 5 AC1 25 GLN A 201 VAL A 225 LEU A 227 HOH A 603 SITE 6 AC1 25 HOH A 619 HOH A 654 HOH A 689 HOH A 715 SITE 7 AC1 25 HOH A 791 SITE 1 AC2 2 ILE A 34 GLU A 118 SITE 1 AC3 7 ARG A 105 ALA A 123 ALA A 124 ASN A 125 SITE 2 AC3 7 ASP A 128 HOH A 645 HOH A 729 SITE 1 AC4 7 ILE A 386 GLU A 389 LYS A 390 GLN A 391 SITE 2 AC4 7 TYR A 396 GLU A 402 HOH A 614 SITE 1 AC5 4 PHE A 398 ARG A 403 HOH A 615 HOH A 695 SITE 1 AC6 24 TYR B 37 GLY B 39 ASP B 41 GLY B 50 SITE 2 AC6 24 HIS B 51 PRO B 54 LEU B 71 THR B 76 SITE 3 AC6 24 ASP B 81 TYR B 175 GLN B 179 ASP B 182 SITE 4 AC6 24 GLN B 195 GLY B 197 GLY B 198 ASP B 200 SITE 5 AC6 24 GLN B 201 VAL B 225 PRO B 226 LEU B 227 SITE 6 AC6 24 HOH B 604 HOH B 615 HOH B 646 HOH B 687 CRYST1 81.622 64.613 89.670 90.00 100.98 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 0.012252 0.000000 0.002377 0.00000 SCALE2 0.000000 0.015477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011360 0.00000