HEADER LIGASE 09-AUG-18 6HB5 TITLE CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L-TYROSYL) TITLE 2 SULFAMOYL-CYTIDINE 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 (STRAIN B / 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 6HB5 1 REMARK REVDAT 2 24-APR-19 6HB5 1 JRNL REVDAT 1 17-APR-19 6HB5 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. 1.88 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 74837 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2103 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.70 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 5509 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2165 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5369 REMARK 3 BIN R VALUE (WORKING SET) : 0.2162 REMARK 3 BIN FREE R VALUE : 0.2286 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.54 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 140 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 : 6462 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 608 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.98860 REMARK 3 B22 (A**2) : -10.87260 REMARK 3 B33 (A**2) : 0.88390 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.57680 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.250 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.147 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.132 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.143 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.131 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 : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6677 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9037 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2326 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 195 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 996 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6677 ; 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 : 858 ; 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 : 8400 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.30 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.47 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|5 - A|252 } REMARK 3 ORIGIN FOR THE GROUP (A): -50.0233 1.8472 -45.7999 REMARK 3 T TENSOR REMARK 3 T11: 0.1188 T22: 0.1357 REMARK 3 T33: 0.1488 T12: 0.0019 REMARK 3 T13: -0.0056 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.3346 L22: 0.7803 REMARK 3 L33: 0.8266 L12: 0.0507 REMARK 3 L13: 0.2797 L23: -0.2113 REMARK 3 S TENSOR REMARK 3 S11: -0.0161 S12: 0.1689 S13: 0.0519 REMARK 3 S21: -0.0296 S22: 0.0182 S23: 0.0261 REMARK 3 S31: -0.0240 S32: -0.0221 S33: -0.0021 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|253 - A|424 } REMARK 3 ORIGIN FOR THE GROUP (A): -85.1391 5.2374 -57.9560 REMARK 3 T TENSOR REMARK 3 T11: 0.1515 T22: 0.2057 REMARK 3 T33: 0.1834 T12: -0.0097 REMARK 3 T13: -0.0069 T23: 0.0398 REMARK 3 L TENSOR REMARK 3 L11: 2.8250 L22: 0.2119 REMARK 3 L33: 0.6969 L12: -0.1957 REMARK 3 L13: 0.1177 L23: -0.0170 REMARK 3 S TENSOR REMARK 3 S11: 0.0210 S12: 0.3343 S13: 0.0575 REMARK 3 S21: 0.0666 S22: -0.0436 S23: 0.0077 REMARK 3 S31: -0.0339 S32: 0.1390 S33: 0.0225 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|5 - B|252 } REMARK 3 ORIGIN FOR THE GROUP (A): -37.4997 2.2051 -9.2407 REMARK 3 T TENSOR REMARK 3 T11: 0.1904 T22: 0.2240 REMARK 3 T33: 0.1524 T12: 0.0141 REMARK 3 T13: 0.0069 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.9767 L22: 0.4662 REMARK 3 L33: 2.1343 L12: -0.0164 REMARK 3 L13: 1.3422 L23: -0.0492 REMARK 3 S TENSOR REMARK 3 S11: -0.0217 S12: -0.1869 S13: -0.0204 REMARK 3 S21: 0.0801 S22: 0.0281 S23: 0.0112 REMARK 3 S31: -0.0731 S32: -0.1375 S33: -0.0064 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|253 - B|386 } REMARK 3 ORIGIN FOR THE GROUP (A): -7.4198 7.6778 4.0711 REMARK 3 T TENSOR REMARK 3 T11: 0.2077 T22: 0.3444 REMARK 3 T33: 0.3185 T12: -0.0414 REMARK 3 T13: 0.0350 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 2.4188 L22: 3.8687 REMARK 3 L33: 0.8282 L12: -0.9550 REMARK 3 L13: -0.8539 L23: 0.5641 REMARK 3 S TENSOR REMARK 3 S11: 0.0863 S12: 0.0003 S13: 0.2156 REMARK 3 S21: -0.3232 S22: -0.0010 S23: -0.9181 REMARK 3 S31: -0.1734 S32: 0.1301 S33: -0.0853 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { B|387 - B|424 } REMARK 3 ORIGIN FOR THE GROUP (A): 10.7060 3.1763 -1.6137 REMARK 3 T TENSOR REMARK 3 T11: 0.2582 T22: 0.5369 REMARK 3 T33: 0.9823 T12: 0.0453 REMARK 3 T13: 0.2445 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 3.7726 L22: 0.0000 REMARK 3 L33: 3.8321 L12: 5.1638 REMARK 3 L13: 0.7039 L23: 0.1634 REMARK 3 S TENSOR REMARK 3 S11: -0.1119 S12: -0.0983 S13: -0.7373 REMARK 3 S21: -0.0575 S22: 0.1301 S23: -0.8440 REMARK 3 S31: 0.0342 S32: 0.7377 S33: -0.0182 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011029. 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 : 6.5 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) : 0.968625 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 : 98934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 88.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 1.17700 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: NULL 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 (%): 50.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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) EG. FOR SOAKING CRYSTALS REMARK 280 WERE TRANSFERRED TO DROP CONTAINING MOTHER LIQUOR SUPPLEMENTED REMARK 280 WITH 2 MM INHIBITOR., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 32.52450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 ASP A 290 REMARK 465 LYS A 291 REMARK 465 ASN A 292 REMARK 465 SER A 293 REMARK 465 GLY A 294 REMARK 465 LYS A 295 REMARK 465 ALA A 296 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 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 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 240 CG CD OE1 OE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 TYR A 301 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 ARG B 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 158 CG CD CE NZ REMARK 470 ARG B 163 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 164 CG CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 MET B 353 CG SD CE REMARK 470 GLU B 354 CG CD OE1 OE2 REMARK 470 LEU B 359 CG CD1 CD2 REMARK 470 ARG B 372 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 376 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 PHE B 397 CG CD1 CD2 CE1 CE2 CZ 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 GLU B 401 CG CD OE1 OE2 REMARK 470 LYS B 415 CG CD CE NZ REMARK 470 LYS B 416 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 46.51 37.66 REMARK 500 ASP A 346 3.55 -159.59 REMARK 500 ARG A 407 -33.17 -130.32 REMARK 500 ASP B 21 68.32 30.17 REMARK 500 SER B 83 109.50 -44.31 REMARK 500 ASP B 346 2.09 -161.99 REMARK 500 ARG B 407 -11.81 -154.65 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 YSC 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 YSC B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HB7 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH Y3U REMARK 900 RELATED ID: 6HB6 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH YSU DBREF1 6HB5 A 1 424 UNP A0A140NBN7_ECOBD DBREF2 6HB5 A A0A140NBN7 1 424 DBREF1 6HB5 B 1 424 UNP A0A140NBN7_ECOBD DBREF2 6HB5 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 YSC A 501 33 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET CL A 505 1 HET YSC B 501 33 HETNAM YSC [(2~{R},3~{S},4~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE- HETNAM 2 YSC PYRIMIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 YSC ~{N}-[(2~{S})-2-AZANYL-3-(4-HYDROXYPHENYL) HETNAM 4 YSC PROPANOYL]SULFAMATE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 YSC 2(C18 H23 N5 O9 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 ASN A 153 LEU A 161 5 9 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 GLU A 288 1 10 HELIX 20 AC2 ARG A 298 GLY A 330 1 33 HELIX 21 AC3 SER A 336 ASP A 346 1 11 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 LEU B 6 ARG B 13 1 8 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 CYS B 116 SER B 120 5 5 HELIX 32 AD5 ASN B 126 GLY B 131 1 6 HELIX 33 AD6 ASN B 134 ILE B 142 1 9 HELIX 34 AD7 GLY B 143 PHE B 146 5 4 HELIX 35 AD8 SER B 147 ILE B 152 1 6 HELIX 36 AD9 LYS B 154 GLN B 159 1 6 HELIX 37 AE1 ARG B 160 ASN B 162 5 3 HELIX 38 AE2 ARG B 163 GLY B 167 5 5 HELIX 39 AE3 SER B 169 GLY B 191 1 23 HELIX 40 AE4 GLN B 201 GLN B 217 1 17 HELIX 41 AE5 SER B 252 ASN B 262 1 11 HELIX 42 AE6 ALA B 264 THR B 276 1 13 HELIX 43 AE7 SER B 279 SER B 293 1 15 HELIX 44 AE8 ARG B 298 GLY B 330 1 33 HELIX 45 AE9 SER B 336 ASP B 346 1 11 HELIX 46 AF1 ASP B 358 SER B 366 1 9 HELIX 47 AF2 SER B 371 SER B 381 1 11 HELIX 48 AF3 ARG B 403 GLY B 406 5 4 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 LEU A 71 N CYS A 38 SHEET 6 AA1 6 ILE A 122 ASN A 125 1 O ILE A 122 N ALA A 70 SHEET 1 AA2 5 MET A 350 MET A 353 0 SHEET 2 AA2 5 ASN A 417 TRP A 423 1 O LEU A 420 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 LEU A 227 HOH A 603 HOH A 623 SITE 6 AC1 25 HOH A 652 HOH A 700 HOH A 712 HOH A 750 SITE 7 AC1 25 HOH A 832 SITE 1 AC2 2 PRO A 33 HOH A 806 SITE 1 AC3 3 PRO A 110 PHE A 111 LEU A 310 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 612 SITE 1 AC5 4 PHE A 398 ARG A 403 HOH A 622 HOH A 676 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 LEU B 227 HOH B 603 HOH B 604 SITE 6 AC6 24 HOH B 620 HOH B 655 HOH B 658 HOH B 683 CRYST1 81.611 65.049 90.686 90.00 101.35 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 0.012253 0.000000 0.002460 0.00000 SCALE2 0.000000 0.015373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011247 0.00000