HEADER HYDROLASE/DNA/ANTIBIOTIC 16-FEB-17 5UUH TITLE BACILLUS CEREUS DNA GLYCOSYLASE ALKD BOUND TO A YATAKEMYCIN-ADENINE TITLE 2 NUCLEOBASE ADDUCT AND DNA CONTAINING A FLUORINATED ABASIC SITE (9-MER TITLE 3 PRODUCT COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-7-METHYLGUANINE GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKD; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*GP*GP*CP*AP*(ORF)P*AP*GP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 ATCC: 14579; SOURCE 5 GENE: BCERE0015_46090; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBG103; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DNA GLYCOSYLASE, PROTEIN-DNA COMPLEX, ALKYLPURINE, BULKY LESION, KEYWDS 2 HYDROLASE-DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.MULLINS,B.F.EICHMAN REVDAT 7 04-OCT-23 5UUH 1 HETSYN LINK REVDAT 6 29-JUL-20 5UUH 1 REMARK LINK SITE REVDAT 5 27-NOV-19 5UUH 1 REMARK REVDAT 4 13-SEP-17 5UUH 1 REMARK REVDAT 3 30-AUG-17 5UUH 1 JRNL REVDAT 2 16-AUG-17 5UUH 1 JRNL REVDAT 1 19-JUL-17 5UUH 0 JRNL AUTH E.A.MULLINS,R.SHI,B.F.EICHMAN JRNL TITL TOXICITY AND REPAIR OF DNA ADDUCTS PRODUCED BY THE NATURAL JRNL TITL 2 PRODUCT YATAKEMYCIN. JRNL REF NAT. CHEM. BIOL. V. 13 1002 2017 JRNL REFN ESSN 1552-4469 JRNL PMID 28759018 JRNL DOI 10.1038/NCHEMBIO.2439 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 43320 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2172 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 36.4322 - 3.9517 0.99 2652 136 0.1327 0.1501 REMARK 3 2 3.9517 - 3.1371 1.00 2610 139 0.1297 0.1591 REMARK 3 3 3.1371 - 2.7407 1.00 2584 139 0.1369 0.1779 REMARK 3 4 2.7407 - 2.4902 1.00 2582 137 0.1360 0.1927 REMARK 3 5 2.4902 - 2.3117 1.00 2586 132 0.1305 0.1388 REMARK 3 6 2.3117 - 2.1755 1.00 2559 138 0.1288 0.1446 REMARK 3 7 2.1755 - 2.0665 1.00 2583 140 0.1360 0.1673 REMARK 3 8 2.0665 - 1.9766 1.00 2580 138 0.1479 0.1930 REMARK 3 9 1.9766 - 1.9005 1.00 2568 134 0.1498 0.1648 REMARK 3 10 1.9005 - 1.8349 1.00 2564 134 0.1499 0.2133 REMARK 3 11 1.8349 - 1.7775 1.00 2549 138 0.1607 0.2160 REMARK 3 12 1.7775 - 1.7267 1.00 2585 126 0.1684 0.2240 REMARK 3 13 1.7267 - 1.6813 1.00 2533 136 0.1677 0.2245 REMARK 3 14 1.6813 - 1.6403 1.00 2580 135 0.1737 0.1939 REMARK 3 15 1.6403 - 1.6030 1.00 2551 139 0.1843 0.2372 REMARK 3 16 1.6030 - 1.5689 0.97 2482 131 0.2075 0.2442 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.75 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 : 0.010 2462 REMARK 3 ANGLE : 1.305 3428 REMARK 3 CHIRALITY : 0.054 358 REMARK 3 PLANARITY : 0.008 368 REMARK 3 DIHEDRAL : 18.388 924 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8214 -5.9043 37.8776 REMARK 3 T TENSOR REMARK 3 T11: 0.2523 T22: 0.4076 REMARK 3 T33: 0.1546 T12: 0.0007 REMARK 3 T13: -0.0191 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 4.0963 L22: 0.9270 REMARK 3 L33: 0.0391 L12: 1.2393 REMARK 3 L13: 0.1182 L23: 0.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.1359 S12: -0.5639 S13: -0.0362 REMARK 3 S21: 0.4382 S22: -0.3025 S23: -0.1578 REMARK 3 S31: -0.0530 S32: 0.4167 S33: 0.0966 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2856 -18.0778 26.4708 REMARK 3 T TENSOR REMARK 3 T11: 0.2887 T22: 0.1891 REMARK 3 T33: 0.1861 T12: 0.0252 REMARK 3 T13: 0.0287 T23: 0.0375 REMARK 3 L TENSOR REMARK 3 L11: 3.4241 L22: 2.2726 REMARK 3 L33: 7.3684 L12: -1.1484 REMARK 3 L13: 0.1440 L23: 0.7475 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: -0.1084 S13: -0.2496 REMARK 3 S21: 0.2410 S22: -0.0947 S23: 0.1417 REMARK 3 S31: 0.9097 S32: -0.0337 S33: 0.1447 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.8195 -0.6218 32.0968 REMARK 3 T TENSOR REMARK 3 T11: 0.1832 T22: 0.3039 REMARK 3 T33: 0.1497 T12: -0.0118 REMARK 3 T13: -0.0289 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.7254 L22: 1.6936 REMARK 3 L33: 2.6906 L12: 0.1049 REMARK 3 L13: -0.9154 L23: 0.1390 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: -0.2113 S13: 0.2530 REMARK 3 S21: 0.1970 S22: -0.0150 S23: -0.1163 REMARK 3 S31: -0.2658 S32: 0.5068 S33: 0.0120 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 103 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.2948 2.5233 21.9037 REMARK 3 T TENSOR REMARK 3 T11: 0.1781 T22: 0.2349 REMARK 3 T33: 0.1579 T12: -0.0114 REMARK 3 T13: -0.0031 T23: -0.0213 REMARK 3 L TENSOR REMARK 3 L11: 1.8293 L22: 1.4758 REMARK 3 L33: 2.4738 L12: 1.4663 REMARK 3 L13: -1.1859 L23: -1.5489 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: -0.2407 S13: 0.1987 REMARK 3 S21: 0.2664 S22: -0.0419 S23: 0.1139 REMARK 3 S31: -0.2889 S32: 0.2611 S33: -0.0226 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 104 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.0611 -0.6766 14.8396 REMARK 3 T TENSOR REMARK 3 T11: 0.1408 T22: 0.1854 REMARK 3 T33: 0.1276 T12: 0.0177 REMARK 3 T13: -0.0086 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.2685 L22: 1.6666 REMARK 3 L33: 1.5652 L12: -0.4204 REMARK 3 L13: 0.0847 L23: -0.8134 REMARK 3 S TENSOR REMARK 3 S11: -0.0776 S12: -0.1454 S13: 0.0120 REMARK 3 S21: 0.1339 S22: 0.0420 S23: 0.0036 REMARK 3 S31: -0.0758 S32: 0.1102 S33: 0.0276 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4847 -0.2777 3.2810 REMARK 3 T TENSOR REMARK 3 T11: 0.1169 T22: 0.1030 REMARK 3 T33: 0.1093 T12: -0.0038 REMARK 3 T13: -0.0040 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 1.0357 L22: 1.3227 REMARK 3 L33: 1.0070 L12: -0.2738 REMARK 3 L13: 0.1142 L23: -0.2966 REMARK 3 S TENSOR REMARK 3 S11: -0.0038 S12: -0.0037 S13: 0.0154 REMARK 3 S21: -0.0472 S22: -0.0223 S23: 0.0010 REMARK 3 S31: 0.0156 S32: 0.0578 S33: 0.0196 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.1221 -3.9395 -3.9487 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.1646 REMARK 3 T33: 0.2233 T12: 0.0156 REMARK 3 T13: -0.0619 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 1.2831 L22: 3.3020 REMARK 3 L33: 1.2720 L12: -0.9832 REMARK 3 L13: -0.1159 L23: 0.4378 REMARK 3 S TENSOR REMARK 3 S11: 0.0475 S12: 0.1526 S13: -0.1374 REMARK 3 S21: -0.2781 S22: -0.1765 S23: 0.4752 REMARK 3 S31: -0.0520 S32: -0.2324 S33: 0.1099 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.2356 -9.5513 15.6937 REMARK 3 T TENSOR REMARK 3 T11: 0.2778 T22: 0.2799 REMARK 3 T33: 0.2346 T12: 0.0110 REMARK 3 T13: 0.0636 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 4.8993 L22: 3.7762 REMARK 3 L33: 4.6178 L12: 0.3454 REMARK 3 L13: 0.0481 L23: 0.7734 REMARK 3 S TENSOR REMARK 3 S11: -0.1427 S12: -0.0293 S13: 0.2591 REMARK 3 S21: 0.6417 S22: 0.0200 S23: 0.4155 REMARK 3 S31: -0.0859 S32: -0.6949 S33: 0.1547 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.1958 -12.7549 16.7282 REMARK 3 T TENSOR REMARK 3 T11: 0.2340 T22: 0.2193 REMARK 3 T33: 0.2119 T12: 0.0023 REMARK 3 T13: 0.0242 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.7078 L22: 2.2245 REMARK 3 L33: 3.9615 L12: -0.0415 REMARK 3 L13: 0.5733 L23: 1.4721 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: -0.2490 S13: 0.0072 REMARK 3 S21: 0.2032 S22: -0.3048 S23: 0.1436 REMARK 3 S31: -0.1367 S32: -0.5715 S33: 0.3073 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 5UUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.569 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% W/V PEG8000, 50 MM HEPES, PH 7.0, REMARK 280 50 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 62.69800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.87400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.69800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.87400 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 VAL A -1 REMARK 465 PRO A 0 REMARK 465 GLY A 226 REMARK 465 ILE A 227 REMARK 465 ASN A 228 REMARK 465 ASN A 229 REMARK 465 GLU A 230 REMARK 465 LYS A 231 REMARK 465 ILE A 232 REMARK 465 GLY A 233 REMARK 465 GLU A 234 REMARK 465 THR A 235 REMARK 465 LEU A 236 REMARK 465 SER A 237 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 O HOH A 472 O HOH A 659 2.15 REMARK 500 OE2 GLU A 101 O HOH A 401 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 3 O5' - P - OP1 ANGL. DEV. = 8.6 DEGREES REMARK 500 DC C 3 O5' - P - OP2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC C 3 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES 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 MET A 28 31.81 -96.22 REMARK 500 THR A 54 158.25 73.82 REMARK 500 TYR A 134 -50.32 -124.11 REMARK 500 LYS A 158 -122.12 51.59 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 444 O REMARK 620 2 HOH A 471 O 79.7 REMARK 620 3 HOH B 205 O 143.0 90.2 REMARK 620 4 HOH B 210 O 139.6 97.2 76.7 REMARK 620 5 HOH B 217 O 71.5 83.2 143.0 68.2 REMARK 620 6 HOH B 230 O 103.7 171.2 91.7 74.9 90.1 REMARK 620 7 HOH C 121 O 69.3 113.0 82.5 143.3 133.4 75.8 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UUF RELATED DB: PDB REMARK 900 RELATED ID: 5UUG RELATED DB: PDB REMARK 900 RELATED ID: 5UUJ RELATED DB: PDB DBREF 5UUH A 1 237 UNP C2T7T7 C2T7T7_BACCE 1 237 DBREF 5UUH B 1 9 PDB 5UUH 5UUH 1 9 DBREF 5UUH C 1 9 PDB 5UUH 5UUH 1 9 SEQADV 5UUH GLY A -3 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUH PRO A -2 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUH VAL A -1 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUH PRO A 0 UNP C2T7T7 EXPRESSION TAG SEQRES 1 A 241 GLY PRO VAL PRO MET HIS PRO PHE VAL LYS ALA LEU GLN SEQRES 2 A 241 GLU HIS PHE THR ALA HIS GLN ASN PRO GLU LYS ALA GLU SEQRES 3 A 241 PRO MET ALA ARG TYR MET LYS ASN HIS PHE LEU PHE LEU SEQRES 4 A 241 GLY ILE GLN THR PRO GLU ARG ARG GLN LEU LEU LYS ASP SEQRES 5 A 241 ILE ILE GLN ILE HIS THR LEU PRO ASP GLN LYS ASP PHE SEQRES 6 A 241 GLN ILE ILE ILE ARG GLU LEU TRP ASP LEU PRO GLU ARG SEQRES 7 A 241 GLU PHE GLN ALA ALA ALA LEU ASP ILE MET GLN LYS TYR SEQRES 8 A 241 LYS LYS HIS ILE ASN GLU THR HIS ILE PRO PHE LEU GLU SEQRES 9 A 241 GLU LEU ILE VAL THR LYS SER TRP TRP ASP SER VAL ASP SEQRES 10 A 241 SER ILE VAL PRO THR PHE LEU GLY ASP ILE PHE LEU LYS SEQRES 11 A 241 HIS PRO GLU LEU ILE SER ALA TYR ILE PRO LYS TRP ILE SEQRES 12 A 241 ALA SER ASP ASN ILE TRP LEU GLN ARG ALA ALA ILE LEU SEQRES 13 A 241 PHE GLN LEU LYS TYR LYS GLN LYS MET ASP GLU GLU LEU SEQRES 14 A 241 LEU PHE TRP ILE ILE GLY GLN LEU HIS SER SER LYS GLU SEQRES 15 A 241 PHE PHE ILE GLN LYS ALA ILE GLY TRP VAL LEU ARG GLU SEQRES 16 A 241 TYR ALA LYS THR ASN PRO ASP VAL VAL TRP GLU TYR VAL SEQRES 17 A 241 GLN ASN ASN GLU LEU ALA PRO LEU SER LYS ARG GLU ALA SEQRES 18 A 241 ILE LYS HIS ILE LYS GLN ASN TYR GLY ILE ASN ASN GLU SEQRES 19 A 241 LYS ILE GLY GLU THR LEU SER SEQRES 1 B 9 DA DG DG DC DA RF5 DA DG DC SEQRES 1 C 9 DT DG DC DT DT DT DG DC DC HET RF5 B 6 20 HET CA A 301 1 HET YTA B 101 93 HETNAM RF5 2-DEOXY-2-FLUORO-5-O-PHOSPHONO-ALPHA-D-ARABINOFURANOSE HETNAM CA CALCIUM ION HETNAM YTA YATAKEMYCIN-ADENINE NUCLEOBASE ADDUCT HETSYN RF5 INHIBITOR ARABINOSYL-2-FLUORO-2-DEOXYNICOTINAMIDE HETSYN 2 RF5 MONONUCLEOTIDE, BOUND FORM; 2-DEOXY-2-FLUORO-5-O- HETSYN 3 RF5 PHOSPHONO-ALPHA-D-ARABINOSE; 2-DEOXY-2-FLUORO-5-O- HETSYN 4 RF5 PHOSPHONO-D-ARABINOSE; 2-DEOXY-2-FLUORO-5-O-PHOSPHONO- HETSYN 5 RF5 ARABINOSE FORMUL 2 RF5 C5 H10 F O7 P FORMUL 4 CA CA 2+ FORMUL 5 YTA C40 H34 N10 O8 S FORMUL 6 HOH *353(H2 O) HELIX 1 AA1 HIS A 2 HIS A 15 1 14 HELIX 2 AA2 ASN A 17 MET A 28 1 12 HELIX 3 AA3 GLN A 38 THR A 54 1 17 HELIX 4 AA4 ASP A 57 LYS A 59 5 3 HELIX 5 AA5 ASP A 60 ASP A 70 1 11 HELIX 6 AA6 GLU A 73 LYS A 86 1 14 HELIX 7 AA7 TYR A 87 ILE A 91 5 5 HELIX 8 AA8 ASN A 92 THR A 94 5 3 HELIX 9 AA9 HIS A 95 THR A 105 1 11 HELIX 10 AB1 TRP A 108 VAL A 116 1 9 HELIX 11 AB2 THR A 118 HIS A 127 1 10 HELIX 12 AB3 PRO A 128 ALA A 133 5 6 HELIX 13 AB4 TYR A 134 SER A 141 1 8 HELIX 14 AB5 ASN A 143 PHE A 153 1 11 HELIX 15 AB6 TYR A 157 MET A 161 5 5 HELIX 16 AB7 ASP A 162 HIS A 174 1 13 HELIX 17 AB8 GLU A 178 ALA A 193 1 16 HELIX 18 AB9 ASN A 196 ASN A 207 1 12 HELIX 19 AC1 ALA A 210 LYS A 219 1 10 HELIX 20 AC2 ILE A 221 TYR A 225 5 5 LINK O3' DA B 5 P RF5 B 6 1555 1555 1.62 LINK O3 RF5 B 6 P DA B 7 1555 1555 1.61 LINK CA CA A 301 O HOH A 444 1555 1555 2.42 LINK CA CA A 301 O HOH A 471 1555 1555 2.47 LINK CA CA A 301 O HOH B 205 1555 1555 2.57 LINK CA CA A 301 O HOH B 210 1555 1555 2.50 LINK CA CA A 301 O HOH B 217 1555 1555 2.51 LINK CA CA A 301 O HOH B 230 1555 1555 2.41 LINK CA CA A 301 O HOH C 121 1555 1555 2.41 CRYST1 125.396 55.748 48.124 90.00 111.18 90.00 C 1 2 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 0.007975 0.000000 0.003090 0.00000 SCALE2 0.000000 0.017938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022285 0.00000