HEADER LIGASE 15-OCT-20 7AP3 TITLE CRYSTAL STRUCTURE OF E. COLI TYROSYL-TRNA SYNTHETASE IN COMPLEX WITH TITLE 2 TYRS7HMDDA 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 STRAIN: DE3; SOURCE 5 GENE: TYRS, ECBD_2006; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 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 2 31-JAN-24 7AP3 1 REMARK REVDAT 1 28-OCT-20 7AP3 0 JRNL AUTH B.ZHANG,L.PANG,M.NAUTIYAL,S.DE GRAEF,B.GADAKH,E.LESCRINIER, JRNL AUTH 2 J.ROZENSKI,S.V.STRELKOV,S.D.WEEKS,A.VAN AERSCHOT JRNL TITL SYNTHESIS AND BIOLOGICAL EVALUATION OF JRNL TITL 2 1,3-DIDEAZAPURINE-LIKE 7-AMINO-5-HYDROXYMETHYL-BENZIMIDAZOLE JRNL TITL 3 RIBONUCLEOSIDE ANALOGUES AS AMINOACYL-TRNA SYNTHETASE JRNL TITL 4 INHIBITORS. JRNL REF MOLECULES V. 25 2020 JRNL REFN ESSN 1420-3049 JRNL PMID 33081246 JRNL DOI 10.3390/MOLECULES25204751 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 63621 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2467 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 54.6810 - 5.2346 0.99 3532 130 0.1795 0.2566 REMARK 3 2 5.2346 - 4.1553 0.98 3381 157 0.1605 0.1926 REMARK 3 3 4.1553 - 3.6301 0.99 3419 117 0.1650 0.2017 REMARK 3 4 3.6301 - 3.2983 0.99 3427 138 0.1899 0.2242 REMARK 3 5 3.2983 - 3.0619 0.99 3396 134 0.2001 0.2200 REMARK 3 6 3.0619 - 2.8814 0.99 3406 145 0.2080 0.2543 REMARK 3 7 2.8814 - 2.7371 0.99 3379 126 0.2112 0.2731 REMARK 3 8 2.7371 - 2.6179 0.99 3384 152 0.2108 0.3200 REMARK 3 9 2.6179 - 2.5172 0.99 3392 143 0.2119 0.2814 REMARK 3 10 2.5172 - 2.4303 1.00 3392 135 0.2229 0.2972 REMARK 3 11 2.4303 - 2.3543 1.00 3405 132 0.2279 0.2858 REMARK 3 12 2.3543 - 2.2870 0.99 3390 127 0.2389 0.2862 REMARK 3 13 2.2870 - 2.2268 0.99 3358 141 0.2493 0.3135 REMARK 3 14 2.2268 - 2.1725 0.99 3381 137 0.2464 0.2858 REMARK 3 15 2.1725 - 2.1231 0.99 3399 138 0.2677 0.3298 REMARK 3 16 2.1231 - 2.0779 0.99 3367 146 0.2800 0.3369 REMARK 3 17 2.0779 - 2.0363 0.99 3351 118 0.2952 0.3613 REMARK 3 18 2.0363 - 2.0000 0.99 3395 151 0.3086 0.3201 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 6635 REMARK 3 ANGLE : 0.844 8988 REMARK 3 CHIRALITY : 0.048 985 REMARK 3 PLANARITY : 0.005 1219 REMARK 3 DIHEDRAL : 7.200 3958 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.0406 2.1689 -9.5796 REMARK 3 T TENSOR REMARK 3 T11: 0.2269 T22: 0.3220 REMARK 3 T33: 0.1884 T12: 0.0119 REMARK 3 T13: -0.0107 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 1.3807 L22: 1.1021 REMARK 3 L33: 2.3963 L12: -0.2159 REMARK 3 L13: 1.4126 L23: -0.4458 REMARK 3 S TENSOR REMARK 3 S11: -0.0507 S12: -0.2231 S13: 0.0296 REMARK 3 S21: 0.1132 S22: 0.0041 S23: 0.0027 REMARK 3 S31: -0.1087 S32: -0.2062 S33: 0.0308 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 243 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2046 7.5725 7.9976 REMARK 3 T TENSOR REMARK 3 T11: 0.3389 T22: 0.3641 REMARK 3 T33: 0.2369 T12: -0.0499 REMARK 3 T13: -0.0899 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 2.7052 L22: 3.6415 REMARK 3 L33: 3.0142 L12: -1.7219 REMARK 3 L13: -1.8328 L23: 1.6630 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: -0.0943 S13: 0.1139 REMARK 3 S21: 0.1933 S22: -0.0049 S23: -0.3119 REMARK 3 S31: -0.1915 S32: 0.2853 S33: 0.0131 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 424 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3119 4.6147 -3.2653 REMARK 3 T TENSOR REMARK 3 T11: 0.4680 T22: 0.7341 REMARK 3 T33: 1.4483 T12: -0.0083 REMARK 3 T13: 0.4925 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.7570 L22: 1.0565 REMARK 3 L33: 0.0701 L12: 1.7023 REMARK 3 L13: -0.3486 L23: -0.2324 REMARK 3 S TENSOR REMARK 3 S11: 0.2823 S12: 0.0263 S13: -0.0589 REMARK 3 S21: -1.0389 S22: -0.0304 S23: -1.8830 REMARK 3 S31: -0.0842 S32: 0.4417 S33: 0.0740 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 5 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): -48.7514 0.9213 -45.1946 REMARK 3 T TENSOR REMARK 3 T11: 0.1946 T22: 0.2099 REMARK 3 T33: 0.2279 T12: 0.0022 REMARK 3 T13: -0.0287 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.0028 L22: 0.9365 REMARK 3 L33: 1.9513 L12: 0.2111 REMARK 3 L13: 0.5785 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: -0.0236 S12: 0.1717 S13: 0.0368 REMARK 3 S21: -0.0625 S22: 0.0310 S23: 0.0167 REMARK 3 S31: -0.0214 S32: 0.0432 S33: -0.0092 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 217 THROUGH 267 ) REMARK 3 ORIGIN FOR THE GROUP (A): -64.0345 7.9659 -54.2067 REMARK 3 T TENSOR REMARK 3 T11: 0.2257 T22: 0.3175 REMARK 3 T33: 0.3351 T12: 0.0187 REMARK 3 T13: -0.0465 T23: 0.0400 REMARK 3 L TENSOR REMARK 3 L11: 2.8367 L22: 0.9403 REMARK 3 L33: 0.6741 L12: 1.5352 REMARK 3 L13: 0.0786 L23: -0.2129 REMARK 3 S TENSOR REMARK 3 S11: -0.0934 S12: 0.3608 S13: 0.6821 REMARK 3 S21: -0.0143 S22: 0.0982 S23: 0.3018 REMARK 3 S31: -0.0956 S32: -0.1485 S33: 0.0022 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 268 THROUGH 424 ) REMARK 3 ORIGIN FOR THE GROUP (A): -86.9529 4.8879 -58.2371 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.2987 REMARK 3 T33: 0.2057 T12: -0.0166 REMARK 3 T13: -0.0318 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 3.4119 L22: 0.4853 REMARK 3 L33: 0.6862 L12: -0.1449 REMARK 3 L13: -0.2237 L23: -0.0006 REMARK 3 S TENSOR REMARK 3 S11: 0.0403 S12: 0.4182 S13: 0.1019 REMARK 3 S21: -0.0013 S22: -0.0616 S23: -0.0264 REMARK 3 S31: -0.0433 S32: 0.1708 S33: -0.0090 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 7AP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111247. 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 : 63743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 REMARK 200 RESOLUTION RANGE LOW (A) : 65.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.90600 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: 4OUD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 PH 6 (1M REMARK 280 STOCK SOLUTION ADJUSTED TO PH 5) AND 20% (V/V) ETHYLENE GLYCOL. REMARK 280 FOR SOAKING CRYSTALS WERE TRANSFERRED TO A DROP CONTAINING REMARK 280 MOTHER LIQUOR SUPPLEMENTED WITH 2 MM INHIBITOR., VAPOR DIFFUSION, 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 32.56200 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: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 PHE A 236 REMARK 465 GLY A 237 REMARK 465 LYS A 238 REMARK 465 THR A 239 REMARK 465 GLU A 240 REMARK 465 GLY A 241 REMARK 465 GLY A 242 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 THR B 239 REMARK 465 GLU B 240 REMARK 465 GLY B 241 REMARK 465 ASP B 290 REMARK 465 GLY B 294 REMARK 465 LYS B 295 REMARK 465 ALA B 296 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 ASN A 5 CG OD1 ND2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 118 CG CD OE1 OE2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 ASN A 162 CG OD1 ND2 REMARK 470 ARG A 214 CD NE CZ NH1 NH2 REMARK 470 THR A 234 OG1 CG2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 LEU A 359 CG CD1 CD2 REMARK 470 GLN A 369 CG CD OE1 NE2 REMARK 470 LYS A 377 CG CD CE NZ REMARK 470 GLU A 389 CD OE1 OE2 REMARK 470 LYS A 415 CG CD CE NZ REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 424 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 GLU B 118 CG CD OE1 OE2 REMARK 470 GLU B 164 CG CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 GLU B 281 OE2 REMARK 470 GLU B 288 CG CD OE1 OE2 REMARK 470 LYS B 291 CG CD CE NZ 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 66.20 39.01 REMARK 500 CYS A 116 32.76 -141.23 REMARK 500 GLN A 166 52.98 -93.52 REMARK 500 THR A 234 -153.19 -164.55 REMARK 500 GLU A 395 23.55 -71.44 REMARK 500 ASP B 115 63.02 -151.08 REMARK 500 ASP B 346 7.13 -159.34 REMARK 500 ASN B 382 34.14 71.95 REMARK 500 ARG B 407 -5.77 -141.05 REMARK 500 LYS B 416 -20.46 -141.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 39 O REMARK 620 2 RRB A 501 O3' 112.0 REMARK 620 3 HOH A 684 O 97.4 121.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 39 O REMARK 620 2 RRB B 501 O3' 112.8 REMARK 620 3 HOH B 614 O 99.4 120.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7AP4 RELATED DB: PDB DBREF1 7AP3 A 1 424 UNP A0A140NBN7_ECOBD DBREF2 7AP3 A A0A140NBN7 1 424 DBREF1 7AP3 B 1 424 UNP A0A140NBN7_ECOBD DBREF2 7AP3 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 RRB A 501 37 HET NA A 502 1 HET RRB B 501 37 HET NA B 502 1 HETNAM RRB [(2~{R},3~{S},4~{R},5~{R})-5-[7-AZANYL-5- HETNAM 2 RRB (HYDROXYMETHYL)BENZIMIDAZOL-1-YL]-3,4-BIS(OXIDANYL) HETNAM 3 RRB OXOLAN-2-YL]METHYL ~{N}-[(2~{S})-2-AZANYL-3-(4- HETNAM 4 RRB HYDROXYPHENYL)PROPANOYL]SULFAMATE HETNAM NA SODIUM ION FORMUL 3 RRB 2(C22 H27 N5 O9 S) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *481(H2 O) HELIX 1 AA1 ASN A 5 GLY A 14 1 10 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 160 ASN A 162 5 3 HELIX 14 AB5 SER A 169 GLY A 191 1 23 HELIX 15 AB6 GLN A 201 GLN A 217 1 17 HELIX 16 AB7 SER A 252 ASN A 262 1 11 HELIX 17 AB8 ASP A 267 THR A 276 1 10 HELIX 18 AB9 SER A 279 SER A 293 1 15 HELIX 19 AC1 ARG A 298 GLY A 330 1 33 HELIX 20 AC2 SER A 331 LEU A 335 5 5 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 163 GLY B 167 5 5 HELIX 38 AE2 SER B 169 SER B 174 1 6 HELIX 39 AE3 SER B 174 GLY B 191 1 18 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 GLU B 289 1 11 HELIX 44 AE8 ARG B 298 GLY B 330 1 33 HELIX 45 AE9 SER B 336 GLY B 347 1 12 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 LYS B 399 GLY B 406 5 8 SHEET 1 AA1 5 ILE A 122 ASN A 125 0 SHEET 2 AA1 5 LYS A 67 VAL A 72 1 N ALA A 70 O ILE A 122 SHEET 3 AA1 5 ALA A 35 PHE A 40 1 N CYS A 38 O LEU A 71 SHEET 4 AA1 5 VAL A 192 GLY A 198 1 O ILE A 196 N TYR A 37 SHEET 5 AA1 5 PHE A 221 VAL A 225 1 O PHE A 221 N VAL A 193 SHEET 1 AA2 5 MET A 350 VAL A 351 0 SHEET 2 AA2 5 ASN A 417 CYS A 422 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 GLY B 197 O VAL B 225 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 MET B 353 0 SHEET 2 AA4 5 ASN B 417 TRP B 423 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 LINK O GLY A 39 NA NA A 502 1555 1555 2.95 LINK O3' RRB A 501 NA NA A 502 1555 1555 2.71 LINK NA NA A 502 O HOH A 684 1555 1555 2.77 LINK O GLY B 39 NA NA B 502 1555 1555 2.84 LINK O3' RRB B 501 NA NA B 502 1555 1555 2.77 LINK NA NA B 502 O HOH B 614 1555 1555 2.81 CRYST1 82.166 65.124 90.978 90.00 101.33 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 0.012170 0.000000 0.002440 0.00000 SCALE2 0.000000 0.015355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011210 0.00000