HEADER HYDROLASE/DNA/ANTIBIOTIC 16-FEB-17 5UUG TITLE BACILLUS CEREUS DNA GLYCOSYLASE ALKD BOUND TO A YATAKEMYCIN-ADENINE TITLE 2 NUCLEOBASE ADDUCT AND DNA CONTAINING AN ABASIC SITE (9-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(*AP*GP*GP*CP*AP*(ORP)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 6 04-OCT-23 5UUG 1 LINK REVDAT 5 27-NOV-19 5UUG 1 REMARK REVDAT 4 13-SEP-17 5UUG 1 REMARK REVDAT 3 30-AUG-17 5UUG 1 JRNL REVDAT 2 16-AUG-17 5UUG 1 JRNL REVDAT 1 19-JUL-17 5UUG 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. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1646 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 44.4487 - 3.9186 1.00 2682 141 0.1312 0.1702 REMARK 3 2 3.9186 - 3.1106 1.00 2611 141 0.1220 0.1725 REMARK 3 3 3.1106 - 2.7174 1.00 2622 136 0.1317 0.1360 REMARK 3 4 2.7174 - 2.4690 1.00 2613 138 0.1324 0.1851 REMARK 3 5 2.4690 - 2.2921 1.00 2591 138 0.1274 0.2034 REMARK 3 6 2.2921 - 2.1569 1.00 2612 139 0.1273 0.1778 REMARK 3 7 2.1569 - 2.0489 1.00 2590 135 0.1392 0.1618 REMARK 3 8 2.0489 - 1.9597 1.00 2595 140 0.1508 0.1804 REMARK 3 9 1.9597 - 1.8843 1.00 2580 134 0.1594 0.2024 REMARK 3 10 1.8843 - 1.8192 1.00 2612 141 0.1638 0.2068 REMARK 3 11 1.8192 - 1.7624 1.00 2578 129 0.1705 0.2281 REMARK 3 12 1.7624 - 1.7120 0.99 2531 134 0.1962 0.2338 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.65 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 : 1.313 3426 REMARK 3 CHIRALITY : 0.054 359 REMARK 3 PLANARITY : 0.008 367 REMARK 3 DIHEDRAL : 18.102 920 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2604 -4.5581 37.7049 REMARK 3 T TENSOR REMARK 3 T11: 0.2422 T22: 0.4111 REMARK 3 T33: 0.2385 T12: 0.0571 REMARK 3 T13: -0.0440 T23: 0.0289 REMARK 3 L TENSOR REMARK 3 L11: 3.9743 L22: 5.8170 REMARK 3 L33: 1.4114 L12: 2.1150 REMARK 3 L13: 0.7219 L23: 0.3572 REMARK 3 S TENSOR REMARK 3 S11: 0.0105 S12: -0.4659 S13: -0.1972 REMARK 3 S21: 0.3550 S22: -0.1275 S23: -0.5639 REMARK 3 S31: 0.1653 S32: 0.4077 S33: 0.1555 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.8147 -18.2421 28.1645 REMARK 3 T TENSOR REMARK 3 T11: 0.3255 T22: 0.2152 REMARK 3 T33: 0.1730 T12: -0.0103 REMARK 3 T13: 0.0358 T23: 0.0403 REMARK 3 L TENSOR REMARK 3 L11: 8.2836 L22: 2.9503 REMARK 3 L33: 4.2713 L12: -0.7978 REMARK 3 L13: 3.5817 L23: -0.7225 REMARK 3 S TENSOR REMARK 3 S11: 0.0177 S12: -0.5542 S13: -0.4859 REMARK 3 S21: 0.2929 S22: -0.2035 S23: 0.1582 REMARK 3 S31: 1.0861 S32: -0.4344 S33: 0.1298 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.1797 -2.7283 30.4605 REMARK 3 T TENSOR REMARK 3 T11: 0.1486 T22: 0.2689 REMARK 3 T33: 0.1205 T12: 0.0548 REMARK 3 T13: -0.0332 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 1.8513 L22: 3.7072 REMARK 3 L33: 2.1795 L12: 0.0690 REMARK 3 L13: -0.4349 L23: 1.2426 REMARK 3 S TENSOR REMARK 3 S11: -0.0130 S12: -0.1835 S13: 0.1228 REMARK 3 S21: 0.1226 S22: 0.0082 S23: -0.2176 REMARK 3 S31: -0.0039 S32: 0.3197 S33: 0.0179 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4341 3.8364 22.0094 REMARK 3 T TENSOR REMARK 3 T11: 0.1321 T22: 0.2423 REMARK 3 T33: 0.1513 T12: 0.0342 REMARK 3 T13: -0.0272 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 1.6850 L22: 4.9213 REMARK 3 L33: 3.6653 L12: 2.6126 REMARK 3 L13: -1.4078 L23: -1.9285 REMARK 3 S TENSOR REMARK 3 S11: 0.0798 S12: -0.1361 S13: 0.1187 REMARK 3 S21: 0.3064 S22: 0.0371 S23: 0.1593 REMARK 3 S31: -0.2422 S32: 0.1165 S33: -0.0848 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.3014 1.4818 4.9975 REMARK 3 T TENSOR REMARK 3 T11: 0.1281 T22: 0.1123 REMARK 3 T33: 0.1083 T12: -0.0005 REMARK 3 T13: -0.0005 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.9679 L22: 1.4440 REMARK 3 L33: 0.9591 L12: -0.4479 REMARK 3 L13: 0.0169 L23: -0.1113 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: -0.0398 S13: 0.0221 REMARK 3 S21: -0.0653 S22: 0.0135 S23: 0.0265 REMARK 3 S31: 0.0045 S32: 0.0481 S33: 0.0127 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 205 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.1140 -5.1626 -3.7027 REMARK 3 T TENSOR REMARK 3 T11: 0.2102 T22: 0.1759 REMARK 3 T33: 0.2362 T12: -0.0033 REMARK 3 T13: -0.0470 T23: -0.0329 REMARK 3 L TENSOR REMARK 3 L11: 2.8445 L22: 3.0934 REMARK 3 L33: 2.4514 L12: -0.5180 REMARK 3 L13: -0.5597 L23: -0.0062 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: 0.1538 S13: -0.0835 REMARK 3 S21: -0.2307 S22: -0.1093 S23: 0.4720 REMARK 3 S31: -0.0405 S32: -0.3123 S33: 0.0480 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.4360 -8.0467 15.5166 REMARK 3 T TENSOR REMARK 3 T11: 0.2059 T22: 0.2557 REMARK 3 T33: 0.1788 T12: -0.0113 REMARK 3 T13: 0.0461 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 5.3846 L22: 4.8846 REMARK 3 L33: 5.2724 L12: -0.2907 REMARK 3 L13: -0.4140 L23: 1.4669 REMARK 3 S TENSOR REMARK 3 S11: -0.1375 S12: -0.0973 S13: 0.0613 REMARK 3 S21: 0.5727 S22: 0.0174 S23: 0.4871 REMARK 3 S31: 0.0530 S32: -0.7656 S33: 0.1547 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.4000 -11.2106 16.5113 REMARK 3 T TENSOR REMARK 3 T11: 0.1927 T22: 0.1936 REMARK 3 T33: 0.1377 T12: 0.0167 REMARK 3 T13: 0.0199 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.5697 L22: 4.3169 REMARK 3 L33: 5.7685 L12: 1.2087 REMARK 3 L13: 0.9608 L23: 3.6881 REMARK 3 S TENSOR REMARK 3 S11: 0.1404 S12: -0.2699 S13: -0.0645 REMARK 3 S21: 0.3021 S22: -0.3159 S23: 0.0822 REMARK 3 S31: 0.1115 S32: -0.5437 S33: 0.2465 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 5UUG 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_1000226483. 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 : 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-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 : 32871 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 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 : 6.500 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 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) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57700 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 (%): 45.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 50 MM HEPES, PH 7.0, 50 REMARK 280 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 62.35750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.83050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.35750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.83050 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: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 B 201 O HOH B 226 2.12 REMARK 500 O MET A 1 O HOH A 401 2.16 REMARK 500 O HOH B 212 O HOH C 101 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 DG B 8 O3' DG B 8 C3' -0.050 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 C 3 O5' - P - OP1 ANGL. DEV. = 9.3 DEGREES REMARK 500 DC C 3 O5' - P - OP2 ANGL. DEV. = -7.6 DEGREES REMARK 500 DC C 3 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 1.8 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 31.53 -96.79 REMARK 500 THR A 54 160.26 73.32 REMARK 500 THR A 118 -67.96 -92.66 REMARK 500 LYS A 158 -121.60 51.50 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 467 O REMARK 620 2 HOH A 524 O 81.9 REMARK 620 3 HOH A 536 O 67.7 82.8 REMARK 620 4 HOH B 205 O 142.2 94.8 74.6 REMARK 620 5 HOH B 210 O 145.8 87.3 142.9 70.8 REMARK 620 6 HOH B 229 O 104.2 170.3 92.5 75.8 91.5 REMARK 620 7 HOH C 120 O 69.4 113.8 130.7 142.3 85.9 75.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 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: 5UUF RELATED DB: PDB REMARK 900 RELATED ID: 5UUH RELATED DB: PDB REMARK 900 RELATED ID: 5UUJ RELATED DB: PDB DBREF 5UUG A 1 237 UNP C2T7T7 C2T7T7_BACCE 1 237 DBREF 5UUG B 1 9 PDB 5UUG 5UUG 1 9 DBREF 5UUG C 1 9 PDB 5UUG 5UUG 1 9 SEQADV 5UUG GLY A -3 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUG PRO A -2 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUG VAL A -1 UNP C2T7T7 EXPRESSION TAG SEQADV 5UUG 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 ORP DA DG DC SEQRES 1 C 9 DT DG DC DT DT DT DG DC DC HET ORP B 6 20 HET CA A 301 1 HET YTA B 101 93 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM CA CALCIUM ION HETNAM YTA YATAKEMYCIN-ADENINE NUCLEOBASE ADDUCT FORMUL 2 ORP C5 H11 O7 P FORMUL 4 CA CA 2+ FORMUL 5 YTA C40 H34 N10 O8 S FORMUL 6 HOH *391(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 LYS A 194 1 17 HELIX 18 AB9 ASN A 196 ASN A 207 1 12 HELIX 19 AC1 ALA A 210 ILE A 218 1 9 HELIX 20 AC2 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 LINK CA CA A 301 O HOH A 467 1555 1555 2.37 LINK CA CA A 301 O HOH A 524 1555 1555 2.30 LINK CA CA A 301 O HOH A 536 1555 1555 2.41 LINK CA CA A 301 O HOH B 205 1555 1555 2.49 LINK CA CA A 301 O HOH B 210 1555 1555 2.58 LINK CA CA A 301 O HOH B 229 1555 1555 2.47 LINK CA CA A 301 O HOH C 120 1555 1555 2.50 SITE 1 AC1 7 HOH A 467 HOH A 524 HOH A 536 HOH B 205 SITE 2 AC1 7 HOH B 210 HOH B 229 HOH C 120 SITE 1 AC2 24 MET A 24 TYR A 27 MET A 28 GLN A 38 SITE 2 AC2 24 TRP A 109 HOH A 495 HOH A 519 HOH A 541 SITE 3 AC2 24 DA B 5 ORP B 6 DA B 7 HOH B 204 SITE 4 AC2 24 HOH B 211 HOH B 213 HOH B 217 HOH B 221 SITE 5 AC2 24 HOH B 222 HOH B 224 DT C 4 DT C 5 SITE 6 AC2 24 DT C 6 DG C 7 DC C 8 DC C 9 CRYST1 124.715 55.661 47.991 90.00 112.20 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 0.008018 0.000000 0.003272 0.00000 SCALE2 0.000000 0.017966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022505 0.00000