HEADER HYDROLASE/DNA 13-JUL-16 5KUB TITLE BACILLUS CEREUS DNA GLYCOSYLASE ALKD BOUND TO 7-METHYLGUANINE TITLE 2 NUCLEOBASE AND DNA CONTAINING AN OXOCARBENIUM-INTERMEDIATE ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-7-METHYLGUANINE GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKD; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174; 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, HEAT-LIKE REPEAT, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.MULLINS,B.F.EICHMAN REVDAT 4 04-OCT-23 5KUB 1 REMARK REVDAT 3 27-NOV-19 5KUB 1 REMARK REVDAT 2 28-SEP-16 5KUB 1 JRNL REVDAT 1 14-SEP-16 5KUB 0 JRNL AUTH Z.D.PARSONS,J.M.BLAND,E.A.MULLINS,B.F.EICHMAN JRNL TITL A CATALYTIC ROLE FOR C-H/ PI INTERACTIONS IN BASE EXCISION JRNL TITL 2 REPAIR BY BACILLUS CEREUS DNA GLYCOSYLASE ALKD. JRNL REF J.AM.CHEM.SOC. V. 138 11485 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 27571247 JRNL DOI 10.1021/JACS.6B07399 REMARK 2 REMARK 2 RESOLUTION. 1.73 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 31900 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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 35.0383 - 3.8461 0.98 2817 146 0.1288 0.1553 REMARK 3 2 3.8461 - 3.0533 0.99 2818 145 0.1381 0.1741 REMARK 3 3 3.0533 - 2.6675 0.99 2796 147 0.1454 0.1811 REMARK 3 4 2.6675 - 2.4237 0.99 2770 146 0.1496 0.1898 REMARK 3 5 2.4237 - 2.2500 0.98 2761 151 0.1379 0.1897 REMARK 3 6 2.2500 - 2.1174 0.98 2752 146 0.1390 0.1785 REMARK 3 7 2.1174 - 2.0113 0.98 2757 140 0.1488 0.2082 REMARK 3 8 2.0113 - 1.9238 0.97 2729 145 0.1530 0.1892 REMARK 3 9 1.9238 - 1.8497 0.96 2713 144 0.1479 0.2124 REMARK 3 10 1.8497 - 1.7859 0.97 2723 145 0.1588 0.2106 REMARK 3 11 1.7859 - 1.7301 0.95 2669 140 0.1599 0.1984 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) : 18.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.43 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 : 0.009 2569 REMARK 3 ANGLE : 1.028 3582 REMARK 3 CHIRALITY : 0.058 384 REMARK 3 PLANARITY : 0.008 372 REMARK 3 DIHEDRAL : 16.578 1447 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.9945 19.2511 65.7112 REMARK 3 T TENSOR REMARK 3 T11: 0.3338 T22: 0.1632 REMARK 3 T33: 0.2389 T12: -0.0052 REMARK 3 T13: 0.0521 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 3.1532 L22: 6.4530 REMARK 3 L33: 5.8444 L12: -1.7462 REMARK 3 L13: 1.2684 L23: -5.0476 REMARK 3 S TENSOR REMARK 3 S11: 0.0955 S12: 0.0848 S13: 0.4460 REMARK 3 S21: 0.3808 S22: -0.1829 S23: 0.0369 REMARK 3 S31: -0.7943 S32: 0.1162 S33: 0.0379 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.3422 5.2172 70.4614 REMARK 3 T TENSOR REMARK 3 T11: 0.1304 T22: 0.1542 REMARK 3 T33: 0.1259 T12: -0.0059 REMARK 3 T13: -0.0206 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 5.8897 L22: 3.6914 REMARK 3 L33: 8.3938 L12: -1.1331 REMARK 3 L13: -4.4837 L23: 2.4643 REMARK 3 S TENSOR REMARK 3 S11: -0.0566 S12: -0.3909 S13: -0.0578 REMARK 3 S21: 0.1605 S22: 0.1353 S23: -0.0980 REMARK 3 S31: 0.0579 S32: 0.4137 S33: -0.0537 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2685 11.0775 62.2015 REMARK 3 T TENSOR REMARK 3 T11: 0.1671 T22: 0.1669 REMARK 3 T33: 0.1808 T12: -0.0058 REMARK 3 T13: -0.0156 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 4.9105 L22: 5.5013 REMARK 3 L33: 8.0395 L12: -0.6870 REMARK 3 L13: 0.8253 L23: -4.2602 REMARK 3 S TENSOR REMARK 3 S11: 0.2075 S12: 0.0836 S13: 0.0105 REMARK 3 S21: -0.1292 S22: 0.1999 S23: 0.5872 REMARK 3 S31: -0.0151 S32: -0.4174 S33: -0.3705 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.1268 18.6169 55.5249 REMARK 3 T TENSOR REMARK 3 T11: 0.2407 T22: 0.0979 REMARK 3 T33: 0.1900 T12: 0.0134 REMARK 3 T13: 0.0483 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 5.2731 L22: 4.0964 REMARK 3 L33: 8.3766 L12: -0.9294 REMARK 3 L13: 2.7899 L23: -3.4114 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: 0.2031 S13: 0.4318 REMARK 3 S21: 0.0812 S22: -0.1222 S23: -0.0280 REMARK 3 S31: -0.4345 S32: 0.1474 S33: 0.1483 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.6658 8.5345 47.0458 REMARK 3 T TENSOR REMARK 3 T11: 0.1893 T22: 0.1514 REMARK 3 T33: 0.1643 T12: -0.0144 REMARK 3 T13: 0.0034 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.6117 L22: 0.9681 REMARK 3 L33: 3.9515 L12: -0.3587 REMARK 3 L13: -0.9674 L23: 0.4481 REMARK 3 S TENSOR REMARK 3 S11: 0.0365 S12: 0.0698 S13: 0.0343 REMARK 3 S21: -0.0786 S22: -0.0018 S23: 0.0067 REMARK 3 S31: -0.1326 S32: -0.1607 S33: -0.0483 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 59.4014 -1.7225 43.1852 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1180 REMARK 3 T33: 0.1024 T12: -0.0360 REMARK 3 T13: 0.0024 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 4.9814 L22: 6.6560 REMARK 3 L33: 3.7230 L12: 1.7146 REMARK 3 L13: 1.9729 L23: 3.3535 REMARK 3 S TENSOR REMARK 3 S11: 0.0414 S12: -0.0314 S13: -0.1194 REMARK 3 S21: -0.1743 S22: -0.0433 S23: 0.1910 REMARK 3 S31: 0.0701 S32: -0.0775 S33: -0.0195 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 69.8243 -3.7816 40.9834 REMARK 3 T TENSOR REMARK 3 T11: 0.1459 T22: 0.0915 REMARK 3 T33: 0.1122 T12: 0.0100 REMARK 3 T13: 0.0123 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 4.6525 L22: 5.2268 REMARK 3 L33: 3.2745 L12: 0.5428 REMARK 3 L13: -1.0544 L23: 0.2951 REMARK 3 S TENSOR REMARK 3 S11: 0.0837 S12: 0.1705 S13: -0.0346 REMARK 3 S21: -0.2671 S22: -0.0035 S23: -0.1481 REMARK 3 S31: 0.2041 S32: 0.2081 S33: -0.0700 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.5845 -15.0222 46.0772 REMARK 3 T TENSOR REMARK 3 T11: 0.1868 T22: 0.1221 REMARK 3 T33: 0.1265 T12: -0.0219 REMARK 3 T13: 0.0175 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.5084 L22: 6.2278 REMARK 3 L33: 1.7115 L12: 0.1176 REMARK 3 L13: -0.1742 L23: 1.2454 REMARK 3 S TENSOR REMARK 3 S11: -0.0754 S12: -0.0248 S13: -0.2176 REMARK 3 S21: 0.0497 S22: 0.0251 S23: 0.0211 REMARK 3 S31: 0.2464 S32: 0.0250 S33: 0.0430 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.4155 -12.0707 63.2132 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.3529 REMARK 3 T33: 0.3323 T12: 0.0578 REMARK 3 T13: 0.0446 T23: 0.1012 REMARK 3 L TENSOR REMARK 3 L11: 0.0928 L22: 3.2337 REMARK 3 L33: 2.3924 L12: -0.4404 REMARK 3 L13: -0.3383 L23: 0.4558 REMARK 3 S TENSOR REMARK 3 S11: -0.3495 S12: -0.6362 S13: -0.5549 REMARK 3 S21: 0.1759 S22: 0.2505 S23: -0.0561 REMARK 3 S31: 0.1461 S32: -0.0973 S33: -0.0401 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.5006 -16.4306 63.5328 REMARK 3 T TENSOR REMARK 3 T11: 0.2381 T22: 0.6132 REMARK 3 T33: 0.7065 T12: 0.0885 REMARK 3 T13: 0.1269 T23: 0.2564 REMARK 3 L TENSOR REMARK 3 L11: 5.0819 L22: 2.4536 REMARK 3 L33: 0.1994 L12: -0.8166 REMARK 3 L13: -0.3410 L23: 0.6942 REMARK 3 S TENSOR REMARK 3 S11: -0.2404 S12: 0.4481 S13: -0.6767 REMARK 3 S21: 0.1284 S22: 0.0987 S23: 0.1081 REMARK 3 S31: 0.1417 S32: 0.0943 S33: -0.0263 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.0231 -7.5479 60.6606 REMARK 3 T TENSOR REMARK 3 T11: 0.2922 T22: 0.4144 REMARK 3 T33: 0.4128 T12: 0.1553 REMARK 3 T13: -0.0335 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 3.8820 L22: 8.8316 REMARK 3 L33: 9.1782 L12: 4.6363 REMARK 3 L13: 0.8342 L23: 2.7025 REMARK 3 S TENSOR REMARK 3 S11: -0.6710 S12: -0.2382 S13: -0.4921 REMARK 3 S21: -0.5885 S22: 0.4330 S23: 1.2021 REMARK 3 S31: -1.0776 S32: -1.0948 S33: 0.1769 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 5KUB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-14 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-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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.10_2155 REMARK 200 STARTING MODEL: PDB ENTRY 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% 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, SITTING 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 46.80150 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: 3100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 447 O HOH A 479 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 477 O HOH A 517 1455 2.16 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 C 2 O3' DG C 2 C3' -0.045 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 DG C 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 3.2 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 54 151.12 72.64 REMARK 500 THR A 118 -73.13 -94.29 REMARK 500 TYR A 134 -46.20 -132.10 REMARK 500 LYS A 158 -118.63 51.52 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 587 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 588 DISTANCE = 6.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MY6 B 101 DBREF 5KUB A 1 237 UNP C2T7T7 C2T7T7_BACCE 1 237 DBREF 5KUB B 1 12 PDB 5KUB 5KUB 1 12 DBREF 5KUB C 1 12 PDB 5KUB 5KUB 1 12 SEQADV 5KUB GLY A -3 UNP C2T7T7 EXPRESSION TAG SEQADV 5KUB PRO A -2 UNP C2T7T7 EXPRESSION TAG SEQADV 5KUB VAL A -1 UNP C2T7T7 EXPRESSION TAG SEQADV 5KUB 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 DG DA NRI DA DG DT DC DC DG SEQRES 1 C 12 DC DG DG DA DC DT DC DT DC DG DG DG HET NRI B 6 21 HET MY6 B 101 19 HETNAM NRI PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL) HETNAM 2 NRI ESTER HETNAM MY6 2-AMINO-7-METHYL-1,7-DIHYDRO-6H-PURIN-6-ONE FORMUL 2 NRI C5 H12 N O5 P FORMUL 4 MY6 C6 H7 N5 O FORMUL 5 HOH *329(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 LEU A 71 1 12 HELIX 6 AA6 GLU A 73 TYR A 87 1 15 HELIX 7 AA7 LYS A 88 ILE A 91 5 4 HELIX 8 AA8 ASN A 92 THR A 94 5 3 HELIX 9 AA9 HIS A 95 VAL A 104 1 10 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 GLY A 226 1 6 LINK O3' DA B 5 P NRI B 6 1555 1555 1.61 LINK O3' NRI B 6 P DA B 7 1555 1555 1.60 SITE 1 AC1 7 TYR A 27 DA B 5 NRI B 6 DA B 7 SITE 2 AC1 7 DT C 6 DC C 7 DT C 8 CRYST1 38.450 93.603 47.991 90.00 112.54 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 0.026008 0.000000 0.010793 0.00000 SCALE2 0.000000 0.010683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022560 0.00000