HEADER HYDROLASE/DNA/ANTIBIOTIC 16-FEB-17 5UUF TITLE BACILLUS CEREUS DNA GLYCOSYLASE ALKD BOUND TO A YATAKEMYCIN-ADENINE TITLE 2 NUCLEOBASE ADDUCT AND DNA CONTAINING AN ABASIC SITE (12-MER PRODUCT TITLE 3 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(*CP*CP*CP*CP*AP*(ORP)P*AP*GP*CP*CP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*CP*GP*GP*GP*CP*TP*TP*TP*GP*GP*GP*G)-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 6 04-OCT-23 5UUF 1 REMARK REVDAT 5 27-NOV-19 5UUF 1 REMARK REVDAT 4 13-SEP-17 5UUF 1 REMARK REVDAT 3 30-AUG-17 5UUF 1 JRNL REVDAT 2 16-AUG-17 5UUF 1 JRNL REVDAT 1 19-JUL-17 5UUF 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. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 41372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2014 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 36.4307 - 3.8835 0.99 2886 144 0.1343 0.1618 REMARK 3 2 3.8835 - 3.0829 1.00 2873 144 0.1393 0.1767 REMARK 3 3 3.0829 - 2.6934 1.00 2848 153 0.1489 0.1672 REMARK 3 4 2.6934 - 2.4472 1.00 2860 141 0.1449 0.1894 REMARK 3 5 2.4472 - 2.2718 1.00 2848 153 0.1434 0.1797 REMARK 3 6 2.2718 - 2.1379 1.00 2862 141 0.1426 0.1876 REMARK 3 7 2.1379 - 2.0308 1.00 2875 141 0.1556 0.1850 REMARK 3 8 2.0308 - 1.9424 1.00 2828 150 0.1693 0.2341 REMARK 3 9 1.9424 - 1.8677 1.00 2831 145 0.1751 0.2154 REMARK 3 10 1.8677 - 1.8032 1.00 2874 136 0.1835 0.2269 REMARK 3 11 1.8032 - 1.7468 1.00 2848 145 0.1978 0.2726 REMARK 3 12 1.7468 - 1.6969 0.99 2788 152 0.2227 0.2595 REMARK 3 13 1.6969 - 1.6522 0.96 2724 141 0.2439 0.2974 REMARK 3 14 1.6522 - 1.6119 0.85 2413 128 0.2720 0.3318 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.17 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 2615 REMARK 3 ANGLE : 1.088 3666 REMARK 3 CHIRALITY : 0.060 387 REMARK 3 PLANARITY : 0.008 377 REMARK 3 DIHEDRAL : 15.344 1449 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.6380 22.7393 21.2247 REMARK 3 T TENSOR REMARK 3 T11: 0.2639 T22: 0.1632 REMARK 3 T33: 0.3037 T12: 0.0844 REMARK 3 T13: 0.0233 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 1.0581 L22: 1.0391 REMARK 3 L33: 0.8456 L12: 0.4308 REMARK 3 L13: 0.8343 L23: -0.0615 REMARK 3 S TENSOR REMARK 3 S11: -0.0974 S12: -0.1837 S13: 0.7604 REMARK 3 S21: 0.1562 S22: 0.0459 S23: 0.1192 REMARK 3 S31: -0.7389 S32: -0.4062 S33: 0.0118 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.7118 9.6155 29.0359 REMARK 3 T TENSOR REMARK 3 T11: 0.1685 T22: 0.3182 REMARK 3 T33: 0.1262 T12: 0.0681 REMARK 3 T13: -0.0116 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.5309 L22: 0.0843 REMARK 3 L33: 0.1476 L12: 0.1106 REMARK 3 L13: -0.2390 L23: -0.0135 REMARK 3 S TENSOR REMARK 3 S11: -0.1501 S12: -0.5651 S13: 0.0742 REMARK 3 S21: 0.1454 S22: 0.1151 S23: -0.0765 REMARK 3 S31: 0.1785 S32: 0.4817 S33: 0.0082 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.1295 17.2271 16.4266 REMARK 3 T TENSOR REMARK 3 T11: 0.1876 T22: 0.1710 REMARK 3 T33: 0.1836 T12: 0.0657 REMARK 3 T13: 0.0010 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 1.0041 L22: 1.4118 REMARK 3 L33: 1.2115 L12: 0.0971 REMARK 3 L13: -0.3865 L23: 0.0614 REMARK 3 S TENSOR REMARK 3 S11: 0.0608 S12: 0.1023 S13: 0.3768 REMARK 3 S21: -0.0966 S22: 0.0506 S23: 0.1123 REMARK 3 S31: -0.2708 S32: -0.1446 S33: 0.0726 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.5131 14.2078 9.9769 REMARK 3 T TENSOR REMARK 3 T11: 0.1728 T22: 0.2651 REMARK 3 T33: 0.1842 T12: 0.0419 REMARK 3 T13: 0.0026 T23: 0.0419 REMARK 3 L TENSOR REMARK 3 L11: 0.9368 L22: 0.2698 REMARK 3 L33: 0.4438 L12: 0.2738 REMARK 3 L13: -0.2662 L23: -0.3420 REMARK 3 S TENSOR REMARK 3 S11: -0.0774 S12: 0.2405 S13: -0.0033 REMARK 3 S21: 0.0108 S22: 0.1504 S23: 0.1053 REMARK 3 S31: 0.0192 S32: -0.2516 S33: -0.0550 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8892 12.6421 0.1394 REMARK 3 T TENSOR REMARK 3 T11: 0.1322 T22: 0.2075 REMARK 3 T33: 0.1469 T12: 0.0178 REMARK 3 T13: 0.0068 T23: 0.0409 REMARK 3 L TENSOR REMARK 3 L11: 0.7394 L22: 1.0907 REMARK 3 L33: 1.1911 L12: -0.4705 REMARK 3 L13: -0.3095 L23: -0.0605 REMARK 3 S TENSOR REMARK 3 S11: 0.0731 S12: 0.2657 S13: 0.0451 REMARK 3 S21: -0.0619 S22: 0.0497 S23: 0.0550 REMARK 3 S31: -0.0833 S32: -0.0563 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7977 3.0767 -1.0158 REMARK 3 T TENSOR REMARK 3 T11: 0.1534 T22: 0.2279 REMARK 3 T33: 0.1333 T12: -0.0014 REMARK 3 T13: -0.0158 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 0.6821 L22: 0.8379 REMARK 3 L33: 0.5423 L12: -0.7202 REMARK 3 L13: 0.0195 L23: -0.2159 REMARK 3 S TENSOR REMARK 3 S11: 0.0781 S12: 0.2820 S13: -0.0577 REMARK 3 S21: -0.0461 S22: -0.0049 S23: 0.1218 REMARK 3 S31: 0.1349 S32: -0.1750 S33: 0.0006 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.4118 1.7962 -3.3591 REMARK 3 T TENSOR REMARK 3 T11: 0.1515 T22: 0.2743 REMARK 3 T33: 0.1407 T12: 0.0344 REMARK 3 T13: -0.0027 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.3150 L22: 0.5734 REMARK 3 L33: 0.3049 L12: -0.0546 REMARK 3 L13: -0.1743 L23: -0.3131 REMARK 3 S TENSOR REMARK 3 S11: 0.0558 S12: 0.2410 S13: -0.0604 REMARK 3 S21: -0.1578 S22: -0.1091 S23: -0.0757 REMARK 3 S31: 0.2229 S32: 0.1048 S33: -0.0002 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 226 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.6366 -8.7278 2.0773 REMARK 3 T TENSOR REMARK 3 T11: 0.2094 T22: 0.1699 REMARK 3 T33: 0.2219 T12: 0.0168 REMARK 3 T13: 0.0062 T23: -0.0638 REMARK 3 L TENSOR REMARK 3 L11: 0.7701 L22: 1.2237 REMARK 3 L33: 0.8894 L12: -0.0719 REMARK 3 L13: 0.2337 L23: -0.3941 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: 0.1843 S13: -0.3955 REMARK 3 S21: -0.0864 S22: -0.0423 S23: 0.0032 REMARK 3 S31: 0.3783 S32: 0.0335 S33: -0.0001 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.6855 -6.1228 18.7654 REMARK 3 T TENSOR REMARK 3 T11: 0.2216 T22: 0.2236 REMARK 3 T33: 0.2928 T12: 0.0820 REMARK 3 T13: -0.0112 T23: 0.0425 REMARK 3 L TENSOR REMARK 3 L11: 0.4027 L22: 1.5473 REMARK 3 L33: 1.1223 L12: -0.7461 REMARK 3 L13: -0.1854 L23: -0.0786 REMARK 3 S TENSOR REMARK 3 S11: -0.2379 S12: -0.3428 S13: -0.6266 REMARK 3 S21: 0.2645 S22: 0.2327 S23: -0.2127 REMARK 3 S31: 0.1377 S32: 0.0401 S33: -0.0467 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.5833 -5.8421 17.6020 REMARK 3 T TENSOR REMARK 3 T11: 0.2275 T22: 0.2559 REMARK 3 T33: 0.3070 T12: 0.0120 REMARK 3 T13: 0.0115 T23: 0.0378 REMARK 3 L TENSOR REMARK 3 L11: 0.5080 L22: 1.9566 REMARK 3 L33: 1.1190 L12: 0.3920 REMARK 3 L13: -0.2297 L23: -0.4653 REMARK 3 S TENSOR REMARK 3 S11: -0.3537 S12: -0.1107 S13: -0.6612 REMARK 3 S21: 0.1085 S22: 0.1167 S23: 0.0714 REMARK 3 S31: 0.0710 S32: -0.0530 S33: -0.0029 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 5UUF 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_1000226482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% W/V PEG4000, 42 MM SODIUM ACETATE, REMARK 280 PH 4.6, 85 MM AMMONIUM ACETATE, 5% V/V GLYCEROL, PH 5.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 47.30350 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 381 O HOH A 533 2.07 REMARK 500 O HOH A 510 O HOH A 543 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 5 O3' DC C 5 C3' -0.037 REMARK 500 DT C 6 O3' DT C 6 C3' -0.042 REMARK 500 DT C 7 O3' DT C 7 C3' -0.042 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 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 THR A 54 157.03 72.20 REMARK 500 TYR A 134 -44.07 -131.07 REMARK 500 LYS A 158 -122.65 54.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 550 DISTANCE = 6.17 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YTA B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UUG RELATED DB: PDB REMARK 900 RELATED ID: 5UUH RELATED DB: PDB REMARK 900 RELATED ID: 5UUJ RELATED DB: PDB DBREF 5UUF A 1 237 UNP C2T7T7 C2T7T7_BACCE 1 237 DBREF 5UUF B 1 12 PDB 5UUF 5UUF 1 12 DBREF 5UUF C 1 12 PDB 5UUF 5UUF 1 12 SEQADV 5UUF GLY A -3 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUF PRO A -2 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUF VAL A -1 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUF 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 12 DC DC DC DC DA ORP DA DG DC DC DC DG SEQRES 1 C 12 DC DG DG DG DC DT DT DT DG DG DG DG HET ORP B 6 20 HET YTA B 101 93 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM YTA YATAKEMYCIN-ADENINE NUCLEOBASE ADDUCT FORMUL 2 ORP C5 H11 O7 P FORMUL 4 YTA C40 H34 N10 O8 S FORMUL 5 HOH *314(H2 O) HELIX 1 AA1 HIS A 2 ALA A 14 1 13 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 HIS A 127 1 20 HELIX 11 AB2 PRO A 128 ALA A 133 5 6 HELIX 12 AB3 TYR A 134 SER A 141 1 8 HELIX 13 AB4 ASN A 143 PHE A 153 1 11 HELIX 14 AB5 TYR A 157 MET A 161 5 5 HELIX 15 AB6 ASP A 162 HIS A 174 1 13 HELIX 16 AB7 GLU A 178 ALA A 193 1 16 HELIX 17 AB8 ASN A 196 ASN A 207 1 12 HELIX 18 AB9 ALA A 210 LYS A 219 1 10 HELIX 19 AC1 ILE A 221 TYR A 225 5 5 LINK O3' DA B 5 P ORP B 6 1555 1555 1.62 LINK O3 ORP B 6 P DA B 7 1555 1555 1.60 SITE 1 AC1 23 PRO A 23 MET A 24 TYR A 27 MET A 28 SITE 2 AC1 23 GLN A 38 TRP A 109 LYS A 156 HOH A 361 SITE 3 AC1 23 HOH A 363 HOH A 421 DA B 5 ORP B 6 SITE 4 AC1 23 DA B 7 HOH B 206 HOH B 207 HOH B 208 SITE 5 AC1 23 HOH B 215 HOH B 219 DT C 6 DT C 7 SITE 6 AC1 23 DT C 8 DG C 9 DG C 10 CRYST1 39.173 94.607 48.167 90.00 111.60 90.00 P 1 21 1 2 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 0.025528 0.000000 0.010109 0.00000 SCALE2 0.000000 0.010570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022330 0.00000