HEADER TRANSFERASE/RNA 09-JUN-23 8JOZ TITLE CRYSTAL STRUCTURE OF CMOM FROM E. COLI COMPLEXED WITH SINEFUNGIN AND TITLE 2 CELLULARLY EXPRESSED TRNA SER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA 5-CARBOXYMETHOXYURIDINE METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CMO5U METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRNA SER (88-MER); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: CMOM, SMTA, YCBD, B0921, JW0904; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCA24N; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 11 ORGANISM_TAXID: 83333; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PBSTNAV KEYWDS METHYLTRANSFERASE, TRNA POST-TRANSCRIPTIONAL MODIFICATION, CMOM KEYWDS 2 MCMO5U, TRANSFERASE-RNA COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.YOO,J.KIM REVDAT 2 04-OCT-23 8JOZ 1 JRNL REVDAT 1 30-AUG-23 8JOZ 0 JRNL AUTH J.YOO,J.LEE,J.KIM JRNL TITL STRUCTURAL BASIS FOR THE SELECTIVE METHYLATION OF JRNL TITL 2 5-CARBOXYMETHOXYURIDINE IN TRNA MODIFICATION. JRNL REF NUCLEIC ACIDS RES. V. 51 9432 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37587716 JRNL DOI 10.1093/NAR/GKAD668 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38921 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 40.7400 - 5.3500 1.00 3012 164 0.1784 0.1771 REMARK 3 2 5.3500 - 4.2500 1.00 2749 149 0.1552 0.1822 REMARK 3 3 4.2500 - 3.7100 1.00 2694 146 0.1686 0.2049 REMARK 3 4 3.7100 - 3.3700 1.00 2656 143 0.1887 0.1936 REMARK 3 5 3.3700 - 3.1300 1.00 2618 142 0.2092 0.2573 REMARK 3 6 3.1300 - 2.9400 1.00 2624 142 0.2096 0.2427 REMARK 3 7 2.9400 - 2.8000 1.00 2605 141 0.2223 0.2296 REMARK 3 8 2.8000 - 2.6800 1.00 2599 141 0.2441 0.3003 REMARK 3 9 2.6800 - 2.5700 1.00 2564 139 0.2575 0.3085 REMARK 3 10 2.5700 - 2.4800 1.00 2571 140 0.2498 0.3045 REMARK 3 11 2.4800 - 2.4100 1.00 2560 138 0.2580 0.2920 REMARK 3 12 2.4100 - 2.3400 1.00 2550 138 0.2491 0.3119 REMARK 3 13 2.3400 - 2.2800 1.00 2537 138 0.2552 0.3148 REMARK 3 14 2.2800 - 2.2200 1.00 2582 139 0.2797 0.3023 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 4253 REMARK 3 ANGLE : 0.955 6188 REMARK 3 CHIRALITY : 0.045 703 REMARK 3 PLANARITY : 0.010 468 REMARK 3 DIHEDRAL : 11.862 1425 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300037960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38928 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 40.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 35.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.05 M SODIUM CACODYLATE TRIHYDRATE PH 6.0, 30% V/V (+/-)-2- REMARK 280 METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 194.84400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 389.68800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 292.26600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 487.11000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.42200 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 194.84400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 389.68800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 487.11000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 292.26600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 97.42200 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 469 LIES ON A SPECIAL POSITION. 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 -15 REMARK 465 ARG A -14 REMARK 465 GLY A -13 REMARK 465 SER A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 THR A -5 REMARK 465 ASP A -4 REMARK 465 PRO A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 ARG A 0 REMARK 465 LYS A 258 REMARK 465 ASP A 259 REMARK 465 LYS A 260 REMARK 465 VAL A 261 REMARK 465 GLY A 262 REMARK 465 LEU A 263 REMARK 465 CYS A 264 REMARK 465 GLY A 265 REMARK 465 ARG A 266 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 166 O HOH A 401 2.17 REMARK 500 NH1 ARG A 129 O HOH A 402 2.18 REMARK 500 N ALA A 1 O HOH A 403 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 17 -64.56 -94.87 REMARK 500 ALA A 88 5.54 -63.24 REMARK 500 ARG A 209 77.03 66.57 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 MG B 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 48 OP1 REMARK 620 2 HOH B 264 O 168.8 REMARK 620 3 HOH B 265 O 96.1 93.3 REMARK 620 4 HOH B 321 O 90.5 83.6 88.2 REMARK 620 5 HOH B 358 O 88.6 82.3 174.9 93.7 REMARK 620 6 HOH B 368 O 93.4 92.8 90.3 176.0 87.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 107 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 59 OP1 REMARK 620 2 HOH B 244 O 82.8 REMARK 620 3 HOH B 266 O 86.2 79.5 REMARK 620 4 HOH B 302 O 166.7 89.7 81.7 REMARK 620 5 HOH B 340 O 87.7 161.0 83.4 96.2 REMARK 620 6 HOH B 360 O 98.6 97.6 174.1 93.2 100.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 246 O REMARK 620 2 HOH B 306 O 93.3 REMARK 620 3 HOH B 333 O 89.9 84.8 REMARK 620 4 HOH B 375 O 168.2 88.0 78.5 REMARK 620 5 HOH B 379 O 103.9 90.8 165.8 87.8 REMARK 620 6 HOH B 380 O 89.5 169.1 84.7 87.0 98.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 245 O REMARK 620 2 HOH B 277 O 84.3 REMARK 620 3 HOH B 298 O 83.2 83.5 REMARK 620 4 HOH B 400 O 92.1 170.0 86.9 REMARK 620 5 HOH B 402 O 167.8 91.4 84.9 90.3 REMARK 620 6 HOH B 405 O 92.3 96.3 175.5 93.0 99.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 226 O REMARK 620 2 HOH B 231 O 91.2 REMARK 620 3 HOH B 295 O 84.8 169.3 REMARK 620 4 HOH B 300 O 99.4 92.2 98.2 REMARK 620 5 HOH B 315 O 78.9 86.0 83.5 177.5 REMARK 620 6 HOH B 404 O 160.6 81.2 99.4 98.8 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 219 O REMARK 620 2 HOH B 224 O 172.8 REMARK 620 3 HOH B 229 O 86.8 99.6 REMARK 620 4 HOH B 251 O 88.6 88.9 82.7 REMARK 620 5 HOH B 273 O 92.6 88.7 107.0 170.3 REMARK 620 6 HOH B 307 O 90.5 82.5 165.0 82.4 87.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 214 O REMARK 620 2 HOH B 253 O 85.5 REMARK 620 3 HOH B 281 O 90.5 162.0 REMARK 620 4 HOH B 341 O 151.4 87.1 88.1 REMARK 620 5 HOH B 344 O 76.4 88.1 74.0 75.8 REMARK 620 6 HOH B 384 O 117.2 81.1 116.1 88.8 161.6 REMARK 620 N 1 2 3 4 5 DBREF 8JOZ A 2 261 UNP P36566 CMOM_ECOLI 2 261 DBREF 8JOZ B 1 76 PDB 8JOZ 8JOZ 1 76 SEQADV 8JOZ MET A -15 UNP P36566 INITIATING METHIONINE SEQADV 8JOZ ARG A -14 UNP P36566 EXPRESSION TAG SEQADV 8JOZ GLY A -13 UNP P36566 EXPRESSION TAG SEQADV 8JOZ SER A -12 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -11 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -10 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -9 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -8 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -7 UNP P36566 EXPRESSION TAG SEQADV 8JOZ HIS A -6 UNP P36566 EXPRESSION TAG SEQADV 8JOZ THR A -5 UNP P36566 EXPRESSION TAG SEQADV 8JOZ ASP A -4 UNP P36566 EXPRESSION TAG SEQADV 8JOZ PRO A -3 UNP P36566 EXPRESSION TAG SEQADV 8JOZ ALA A -2 UNP P36566 EXPRESSION TAG SEQADV 8JOZ LEU A -1 UNP P36566 EXPRESSION TAG SEQADV 8JOZ ARG A 0 UNP P36566 EXPRESSION TAG SEQADV 8JOZ ALA A 1 UNP P36566 EXPRESSION TAG SEQADV 8JOZ GLY A 262 UNP P36566 EXPRESSION TAG SEQADV 8JOZ LEU A 263 UNP P36566 EXPRESSION TAG SEQADV 8JOZ CYS A 264 UNP P36566 EXPRESSION TAG SEQADV 8JOZ GLY A 265 UNP P36566 EXPRESSION TAG SEQADV 8JOZ ARG A 266 UNP P36566 EXPRESSION TAG SEQRES 1 A 282 MET ARG GLY SER HIS HIS HIS HIS HIS HIS THR ASP PRO SEQRES 2 A 282 ALA LEU ARG ALA GLN ASP ARG ASN PHE ASP ASP ILE ALA SEQRES 3 A 282 GLU LYS PHE SER ARG ASN ILE TYR GLY THR THR LYS GLY SEQRES 4 A 282 GLN LEU ARG GLN ALA ILE LEU TRP GLN ASP LEU ASP ARG SEQRES 5 A 282 VAL LEU ALA GLU MET GLY PRO GLN LYS LEU ARG VAL LEU SEQRES 6 A 282 ASP ALA GLY GLY GLY GLU GLY GLN THR ALA ILE LYS MET SEQRES 7 A 282 ALA GLU ARG GLY HIS GLN VAL ILE LEU CYS ASP LEU SER SEQRES 8 A 282 ALA GLN MET ILE ASP ARG ALA LYS GLN ALA ALA GLU ALA SEQRES 9 A 282 LYS GLY VAL SER ASP ASN MET GLN PHE ILE HIS CYS ALA SEQRES 10 A 282 ALA GLN ASP VAL ALA SER HIS LEU GLU THR PRO VAL ASP SEQRES 11 A 282 LEU ILE LEU PHE HIS ALA VAL LEU GLU TRP VAL ALA ASP SEQRES 12 A 282 PRO ARG SER VAL LEU GLN THR LEU TRP SER VAL LEU ARG SEQRES 13 A 282 PRO GLY GLY VAL LEU SER LEU MET PHE TYR ASN ALA HIS SEQRES 14 A 282 GLY LEU LEU MET HIS ASN MET VAL ALA GLY ASN PHE ASP SEQRES 15 A 282 TYR VAL GLN ALA GLY MET PRO LYS LYS LYS LYS ARG THR SEQRES 16 A 282 LEU SER PRO ASP TYR PRO ARG ASP PRO ALA GLN VAL TYR SEQRES 17 A 282 LEU TRP LEU GLU GLU ALA GLY TRP GLN ILE MET GLY LYS SEQRES 18 A 282 THR GLY VAL ARG VAL PHE HIS ASP TYR LEU ARG GLU LYS SEQRES 19 A 282 HIS GLN GLN ARG ASP CYS TYR GLU ALA LEU LEU GLU LEU SEQRES 20 A 282 GLU THR ARG TYR CYS ARG GLN GLU PRO TYR ILE THR LEU SEQRES 21 A 282 GLY ARG TYR ILE HIS VAL THR ALA ARG LYS PRO GLN SER SEQRES 22 A 282 LYS ASP LYS VAL GLY LEU CYS GLY ARG SEQRES 1 B 88 G G A A G U G 4SU G G C C G SEQRES 2 B 88 A G C OMG G H2U H2U G A A G G C SEQRES 3 B 88 A C C G G U OMC U CM0 G A ZJS A SEQRES 4 B 88 A C C G G C G A C C C G A SEQRES 5 B 88 A A G G G U U C C A G A G SEQRES 6 B 88 5MU PSU C G A A U C U C U G C SEQRES 7 B 88 G C U U C C G C C A HET 4SU B 8 20 HET OMG B 18 24 HET H2U B 20 20 HET H2U B 20A 20 HET OMC B 32 21 HET CM0 B 34 25 HET ZJS B 37 27 HET 5MU B 54 21 HET PSU B 55 20 HET SFG A 301 27 HET MG B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG B 104 1 HET MG B 105 1 HET MG B 106 1 HET MG B 107 1 HETNAM 4SU 4-THIOURIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM CM0 5-(CARBOXYMETHOXY) URIDINE-5'-MONOPHOSPHATE HETNAM ZJS N-(3-METHYLBUT-2-EN-1-YL)ADENOSINE 5'-(DIHYDROGEN HETNAM 2 ZJS PHOSPHATE) HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM SFG SINEFUNGIN HETNAM MG MAGNESIUM ION HETSYN SFG ADENOSYL-ORNITHINE FORMUL 2 4SU C9 H13 N2 O8 P S FORMUL 2 OMG C11 H16 N5 O8 P FORMUL 2 H2U 2(C9 H15 N2 O9 P) FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 2 CM0 C11 H15 N2 O12 P FORMUL 2 ZJS C15 H22 N5 O7 P FORMUL 2 5MU C10 H15 N2 O9 P FORMUL 2 PSU C9 H13 N2 O9 P FORMUL 3 SFG C15 H23 N7 O5 FORMUL 4 MG 7(MG 2+) FORMUL 11 HOH *351(H2 O) HELIX 1 AA1 PHE A 6 ASP A 8 5 3 HELIX 2 AA2 ILE A 9 ILE A 17 1 9 HELIX 3 AA3 THR A 20 MET A 41 1 22 HELIX 4 AA4 GLY A 56 ARG A 65 1 10 HELIX 5 AA5 SER A 75 ALA A 88 1 14 HELIX 6 AA6 LYS A 89 GLY A 90 5 2 HELIX 7 AA7 VAL A 91 ASP A 93 5 3 HELIX 8 AA8 ALA A 101 LEU A 109 5 9 HELIX 9 AA9 VAL A 121 VAL A 125 5 5 HELIX 10 AB1 ASP A 127 VAL A 138 1 12 HELIX 11 AB2 ASN A 151 GLY A 163 1 13 HELIX 12 AB3 ASN A 164 ALA A 170 1 7 HELIX 13 AB4 ASP A 187 ALA A 198 1 12 HELIX 14 AB5 PHE A 211 LEU A 215 5 5 HELIX 15 AB6 HIS A 219 CYS A 224 1 6 HELIX 16 AB7 CYS A 224 CYS A 236 1 13 HELIX 17 AB8 PRO A 240 GLY A 245 1 6 SHEET 1 AA1 7 MET A 95 ILE A 98 0 SHEET 2 AA1 7 GLN A 68 CYS A 72 1 N LEU A 71 O GLN A 96 SHEET 3 AA1 7 ARG A 47 ALA A 51 1 N ASP A 50 O ILE A 70 SHEET 4 AA1 7 VAL A 113 HIS A 119 1 O LEU A 117 N LEU A 49 SHEET 5 AA1 7 LEU A 139 TYR A 150 1 O SER A 146 N ILE A 116 SHEET 6 AA1 7 TYR A 247 ARG A 253 -1 O VAL A 250 N LEU A 147 SHEET 7 AA1 7 GLN A 201 VAL A 208 -1 N MET A 203 O THR A 251 LINK O3' G B 7 P 4SU B 8 1555 1555 1.61 LINK O3' 4SU B 8 P G B 9 1555 1555 1.61 LINK O3' C B 16 P OMG B 18 1555 1555 1.61 LINK O3' OMG B 18 P G B 19 1555 1555 1.61 LINK O3' G B 19 P H2U B 20 1555 1555 1.60 LINK O3' H2U B 20 P H2U B 20A 1555 1555 1.61 LINK O3' H2U B 20A P G B 20B 1555 1555 1.61 LINK O3' U B 31 P OMC B 32 1555 1555 1.61 LINK O3' OMC B 32 P U B 33 1555 1555 1.61 LINK O3' U B 33 P CM0 B 34 1555 1555 1.61 LINK O3' CM0 B 34 P G B 35 1555 1555 1.59 LINK O3' A B 36 P ZJS B 37 1555 1555 1.61 LINK O3' ZJS B 37 P A B 38 1555 1555 1.61 LINK O3' G B 53 P 5MU B 54 1555 1555 1.61 LINK O3' 5MU B 54 P PSU B 55 1555 1555 1.61 LINK O3' PSU B 55 P C B 56 1555 1555 1.61 LINK OP1 C B 48 MG MG B 105 1555 1555 2.13 LINK OP1 A B 59 MG MG B 107 1555 1555 2.02 LINK MG MG B 101 O HOH B 246 1555 1555 2.07 LINK MG MG B 101 O HOH B 306 1555 1555 2.09 LINK MG MG B 101 O HOH B 333 1555 1555 2.02 LINK MG MG B 101 O HOH B 375 1555 1555 2.27 LINK MG MG B 101 O HOH B 379 1555 1555 2.01 LINK MG MG B 101 O HOH B 380 1555 1555 2.07 LINK MG MG B 102 O HOH B 245 1555 1555 2.22 LINK MG MG B 102 O HOH B 277 1555 1555 1.91 LINK MG MG B 102 O HOH B 298 1555 1555 2.31 LINK MG MG B 102 O HOH B 400 1555 1555 2.17 LINK MG MG B 102 O HOH B 402 1555 1555 2.00 LINK MG MG B 102 O HOH B 405 1555 1555 2.11 LINK MG MG B 103 O HOH B 226 1555 1555 2.09 LINK MG MG B 103 O HOH B 231 1555 1555 2.30 LINK MG MG B 103 O HOH B 295 1555 1555 2.18 LINK MG MG B 103 O HOH B 300 1555 1555 2.05 LINK MG MG B 103 O HOH B 315 1555 1555 2.17 LINK MG MG B 103 O HOH B 404 1555 1555 1.88 LINK MG MG B 104 O HOH B 219 1555 1555 2.13 LINK MG MG B 104 O HOH B 224 1555 1555 2.08 LINK MG MG B 104 O HOH B 229 1555 1555 1.86 LINK MG MG B 104 O HOH B 251 1555 1555 2.33 LINK MG MG B 104 O HOH B 273 1555 1555 1.99 LINK MG MG B 104 O HOH B 307 1555 1555 2.14 LINK MG MG B 105 O HOH B 264 1555 1555 2.13 LINK MG MG B 105 O HOH B 265 1555 1555 1.94 LINK MG MG B 105 O HOH B 321 1555 1555 2.01 LINK MG MG B 105 O HOH B 358 1555 1555 2.27 LINK MG MG B 105 O HOH B 368 1555 1555 2.18 LINK MG MG B 106 O HOH B 214 1555 1555 2.17 LINK MG MG B 106 O HOH B 253 1555 1555 2.02 LINK MG MG B 106 O HOH B 281 1555 1555 2.18 LINK MG MG B 106 O HOH B 341 1555 1555 2.02 LINK MG MG B 106 O HOH B 344 1555 1555 2.27 LINK MG MG B 106 O HOH B 384 1555 1555 2.51 LINK MG MG B 107 O HOH B 244 1555 1555 1.97 LINK MG MG B 107 O HOH B 266 1555 1555 2.06 LINK MG MG B 107 O HOH B 302 1555 1555 1.85 LINK MG MG B 107 O HOH B 340 1555 1555 2.22 LINK MG MG B 107 O HOH B 360 1555 1555 2.05 CISPEP 1 GLU A 239 PRO A 240 0 -2.37 CRYST1 65.614 65.614 584.532 90.00 90.00 120.00 P 61 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015241 0.008799 0.000000 0.00000 SCALE2 0.000000 0.017598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001711 0.00000