HEADER HYDROLASE 12-MAY-16 5JX8 TITLE NEW IMPROVED STRUCTURE OF D4 IN TRIGONAL SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UDG; COMPND 5 EC: 3.2.2.27; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS (STRAIN WESTERN RESERVE); SOURCE 3 ORGANISM_COMMON: VACV; SOURCE 4 ORGANISM_TAXID: 10254; SOURCE 5 STRAIN: WESTERN RESERVE; SOURCE 6 GENE: UNG, TS17, VACWR109, D4R; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS DNA REPAIR ENZYME COMPONENT OF PROCESSIVITY FACTOR POXVIRUS, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,D.CHATTOPADHYAY REVDAT 4 27-SEP-23 5JX8 1 REMARK REVDAT 3 11-DEC-19 5JX8 1 REMARK REVDAT 2 20-SEP-17 5JX8 1 REMARK REVDAT 1 08-FEB-17 5JX8 0 JRNL AUTH N.SCHORMANN,N.ZHUKOVSKAYA,G.BEDWELL,M.NUTH,R.GILLILAN, JRNL AUTH 2 P.E.PREVELIGE,R.P.RICCIARDI,S.BANERJEE,D.CHATTOPADHYAY JRNL TITL POXVIRUS URACIL-DNA GLYCOSYLASE-AN UNUSUAL MEMBER OF THE JRNL TITL 2 FAMILY I URACIL-DNA GLYCOSYLASES. JRNL REF PROTEIN SCI. V. 25 2113 2016 JRNL REFN ESSN 1469-896X JRNL PMID 27684934 JRNL DOI 10.1002/PRO.3058 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2142: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39845 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 19.6207 - 4.7985 0.96 2786 128 0.1688 0.1972 REMARK 3 2 4.7985 - 3.8179 0.99 2759 144 0.1596 0.1954 REMARK 3 3 3.8179 - 3.3380 0.99 2718 141 0.1819 0.2388 REMARK 3 4 3.3380 - 3.0340 1.00 2703 170 0.2163 0.2718 REMARK 3 5 3.0340 - 2.8172 1.00 2674 154 0.2347 0.2912 REMARK 3 6 2.8172 - 2.6515 1.00 2721 138 0.2369 0.2989 REMARK 3 7 2.6515 - 2.5190 1.00 2699 142 0.2280 0.2516 REMARK 3 8 2.5190 - 2.4096 1.00 2692 142 0.2334 0.2971 REMARK 3 9 2.4096 - 2.3170 1.00 2700 138 0.2212 0.2642 REMARK 3 10 2.3170 - 2.2371 1.00 2673 139 0.2281 0.3252 REMARK 3 11 2.2371 - 2.1673 1.00 2699 139 0.2498 0.3024 REMARK 3 12 2.1673 - 2.1054 1.00 2670 142 0.2759 0.3401 REMARK 3 13 2.1054 - 2.0500 1.00 2650 159 0.2963 0.3352 REMARK 3 14 2.0500 - 2.0001 1.00 2703 122 0.3091 0.3537 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.40 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 : 0.007 3748 REMARK 3 ANGLE : 0.920 5092 REMARK 3 CHIRALITY : 0.052 555 REMARK 3 PLANARITY : 0.006 638 REMARK 3 DIHEDRAL : 13.140 2218 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -8 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2767 13.7844 -4.2144 REMARK 3 T TENSOR REMARK 3 T11: 0.3903 T22: 0.4935 REMARK 3 T33: 0.4449 T12: 0.1110 REMARK 3 T13: -0.0090 T23: 0.1105 REMARK 3 L TENSOR REMARK 3 L11: 0.0331 L22: 0.0191 REMARK 3 L33: 0.0299 L12: 0.0197 REMARK 3 L13: 0.0354 L23: 0.0098 REMARK 3 S TENSOR REMARK 3 S11: -0.0292 S12: 0.0189 S13: -0.0529 REMARK 3 S21: -0.1218 S22: -0.0260 S23: -0.2651 REMARK 3 S31: 0.0186 S32: 0.0751 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.7804 12.0080 7.4462 REMARK 3 T TENSOR REMARK 3 T11: 0.2397 T22: 0.4615 REMARK 3 T33: 0.3592 T12: 0.0486 REMARK 3 T13: -0.0524 T23: 0.1085 REMARK 3 L TENSOR REMARK 3 L11: 0.0248 L22: 0.0652 REMARK 3 L33: 0.0259 L12: 0.0036 REMARK 3 L13: -0.0153 L23: -0.0263 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: 0.0169 S13: -0.1443 REMARK 3 S21: -0.1073 S22: 0.0605 S23: 0.0808 REMARK 3 S31: 0.0456 S32: -0.2355 S33: 0.0035 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 71 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5897 16.4752 10.3971 REMARK 3 T TENSOR REMARK 3 T11: 0.2666 T22: 0.4689 REMARK 3 T33: 0.3510 T12: 0.0189 REMARK 3 T13: 0.0496 T23: 0.0739 REMARK 3 L TENSOR REMARK 3 L11: 0.0283 L22: 0.0152 REMARK 3 L33: 0.0365 L12: 0.0001 REMARK 3 L13: 0.0365 L23: -0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.1418 S12: -0.1884 S13: 0.0786 REMARK 3 S21: -0.1418 S22: -0.0069 S23: 0.0091 REMARK 3 S31: -0.0200 S32: 0.0159 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 72 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7615 19.7776 14.5110 REMARK 3 T TENSOR REMARK 3 T11: 0.2573 T22: 0.5903 REMARK 3 T33: 0.3937 T12: -0.0686 REMARK 3 T13: 0.0518 T23: 0.0632 REMARK 3 L TENSOR REMARK 3 L11: 0.1221 L22: 0.0768 REMARK 3 L33: 0.1266 L12: 0.0650 REMARK 3 L13: 0.1240 L23: 0.0733 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: -0.1083 S13: 0.2088 REMARK 3 S21: -0.1975 S22: -0.0819 S23: -0.0533 REMARK 3 S31: -0.3413 S32: 0.1898 S33: -0.0299 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7222 8.3264 15.4148 REMARK 3 T TENSOR REMARK 3 T11: 0.2200 T22: 0.5794 REMARK 3 T33: 0.3510 T12: 0.0223 REMARK 3 T13: 0.0023 T23: 0.1449 REMARK 3 L TENSOR REMARK 3 L11: 0.0076 L22: 0.0154 REMARK 3 L33: 0.0251 L12: 0.0069 REMARK 3 L13: -0.0035 L23: -0.0189 REMARK 3 S TENSOR REMARK 3 S11: 0.1008 S12: -0.1735 S13: -0.0368 REMARK 3 S21: 0.0824 S22: -0.0221 S23: 0.0802 REMARK 3 S31: 0.0094 S32: -0.1086 S33: 0.0092 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 152 THROUGH 168 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5901 8.5620 23.3167 REMARK 3 T TENSOR REMARK 3 T11: 0.2344 T22: 0.5800 REMARK 3 T33: 0.3460 T12: -0.0456 REMARK 3 T13: 0.0464 T23: 0.0884 REMARK 3 L TENSOR REMARK 3 L11: 0.0059 L22: 0.0198 REMARK 3 L33: 0.0042 L12: -0.0127 REMARK 3 L13: 0.0053 L23: -0.0108 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: -0.1126 S13: -0.0186 REMARK 3 S21: 0.0666 S22: -0.0081 S23: 0.1206 REMARK 3 S31: 0.0815 S32: 0.0139 S33: -0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 169 THROUGH 187 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.8345 8.4071 24.4765 REMARK 3 T TENSOR REMARK 3 T11: 0.2967 T22: 0.7702 REMARK 3 T33: 0.4843 T12: -0.1095 REMARK 3 T13: 0.0007 T23: 0.1197 REMARK 3 L TENSOR REMARK 3 L11: 0.0443 L22: 0.0593 REMARK 3 L33: 0.0204 L12: -0.0586 REMARK 3 L13: 0.0243 L23: -0.0312 REMARK 3 S TENSOR REMARK 3 S11: 0.0588 S12: -0.1157 S13: 0.1139 REMARK 3 S21: -0.0274 S22: 0.0834 S23: 0.0199 REMARK 3 S31: 0.0170 S32: -0.0000 S33: -0.0047 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 188 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0588 5.7255 20.9629 REMARK 3 T TENSOR REMARK 3 T11: 0.1896 T22: 0.8510 REMARK 3 T33: 0.4040 T12: 0.0326 REMARK 3 T13: -0.0144 T23: 0.0989 REMARK 3 L TENSOR REMARK 3 L11: 0.0451 L22: 0.0310 REMARK 3 L33: 0.0813 L12: 0.0364 REMARK 3 L13: -0.0589 L23: -0.0491 REMARK 3 S TENSOR REMARK 3 S11: 0.0550 S12: -0.2078 S13: 0.1079 REMARK 3 S21: 0.0762 S22: -0.0403 S23: 0.0103 REMARK 3 S31: -0.0353 S32: 0.0913 S33: 0.0219 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 205 THROUGH 218 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6899 8.3536 9.0490 REMARK 3 T TENSOR REMARK 3 T11: 0.1077 T22: 0.7945 REMARK 3 T33: 0.4157 T12: -0.0477 REMARK 3 T13: 0.1711 T23: 0.1474 REMARK 3 L TENSOR REMARK 3 L11: 0.0939 L22: 0.0868 REMARK 3 L33: 0.0278 L12: 0.0308 REMARK 3 L13: 0.0196 L23: 0.0097 REMARK 3 S TENSOR REMARK 3 S11: 0.1093 S12: 0.0690 S13: -0.0311 REMARK 3 S21: -0.0284 S22: 0.0709 S23: -0.0467 REMARK 3 S31: -0.0680 S32: 0.0730 S33: 0.1020 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -2 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.5205 28.8333 -10.4134 REMARK 3 T TENSOR REMARK 3 T11: 0.4941 T22: 0.3843 REMARK 3 T33: 0.3867 T12: 0.5008 REMARK 3 T13: -0.0128 T23: 0.1031 REMARK 3 L TENSOR REMARK 3 L11: 0.1055 L22: 0.0529 REMARK 3 L33: 0.1551 L12: -0.0387 REMARK 3 L13: -0.0705 L23: 0.0067 REMARK 3 S TENSOR REMARK 3 S11: 0.1837 S12: -0.0478 S13: -0.1200 REMARK 3 S21: -0.0621 S22: -0.0394 S23: 0.1958 REMARK 3 S31: -0.3546 S32: -0.3363 S33: 0.1623 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 87 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.3915 21.6720 -17.4966 REMARK 3 T TENSOR REMARK 3 T11: 0.4967 T22: 0.2280 REMARK 3 T33: 0.3463 T12: 0.5061 REMARK 3 T13: -0.1149 T23: 0.1505 REMARK 3 L TENSOR REMARK 3 L11: 0.0789 L22: 0.0805 REMARK 3 L33: 0.2527 L12: 0.0359 REMARK 3 L13: -0.1330 L23: -0.0800 REMARK 3 S TENSOR REMARK 3 S11: 0.2255 S12: 0.1892 S13: -0.2112 REMARK 3 S21: -0.3748 S22: 0.0391 S23: 0.2145 REMARK 3 S31: -0.1549 S32: -0.5329 S33: 0.1186 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 152 THROUGH 168 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.8239 27.8800 -24.5304 REMARK 3 T TENSOR REMARK 3 T11: 0.6383 T22: 0.3576 REMARK 3 T33: 0.3528 T12: 0.3108 REMARK 3 T13: 0.0201 T23: 0.1206 REMARK 3 L TENSOR REMARK 3 L11: 0.0707 L22: 0.1078 REMARK 3 L33: 0.0322 L12: -0.0544 REMARK 3 L13: 0.0450 L23: -0.0582 REMARK 3 S TENSOR REMARK 3 S11: 0.0522 S12: 0.1511 S13: 0.0582 REMARK 3 S21: -0.1142 S22: -0.0384 S23: 0.0005 REMARK 3 S31: -0.0000 S32: -0.0663 S33: -0.0063 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 169 THROUGH 187 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.3576 23.4734 -25.7054 REMARK 3 T TENSOR REMARK 3 T11: 0.8790 T22: 0.4572 REMARK 3 T33: 0.4985 T12: 0.2904 REMARK 3 T13: 0.0022 T23: 0.0653 REMARK 3 L TENSOR REMARK 3 L11: 0.0412 L22: 0.0176 REMARK 3 L33: 0.0184 L12: -0.0255 REMARK 3 L13: 0.0130 L23: -0.0167 REMARK 3 S TENSOR REMARK 3 S11: 0.1358 S12: 0.0861 S13: 0.0096 REMARK 3 S21: -0.1607 S22: -0.0300 S23: 0.0478 REMARK 3 S31: 0.0131 S32: 0.0347 S33: 0.0000 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 188 THROUGH 218 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7179 14.5846 -17.0436 REMARK 3 T TENSOR REMARK 3 T11: 0.4361 T22: 0.2629 REMARK 3 T33: 0.3837 T12: 0.1615 REMARK 3 T13: 0.0599 T23: 0.0339 REMARK 3 L TENSOR REMARK 3 L11: 0.0316 L22: 0.0722 REMARK 3 L33: 0.1054 L12: -0.0045 REMARK 3 L13: 0.0413 L23: 0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.1787 S12: 0.0757 S13: -0.1017 REMARK 3 S21: -0.2678 S22: 0.0432 S23: -0.2463 REMARK 3 S31: 0.0185 S32: 0.0288 S33: 0.0131 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 5JX8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221372. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MARCH 30, 2013 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2OWQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M (NH4)2SO4, 12% GLYCEROL, 0.1M REMARK 280 HEPES, PH 7.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 92.70000 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 46.35000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.35000 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 92.70000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A -6 CG CD1 CD2 REMARK 470 LYS B 169 CB CG CD CE NZ 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 TYR A 11 -34.83 70.98 REMARK 500 PHE A 79 -13.19 69.43 REMARK 500 ASP A 138 -73.24 -23.36 REMARK 500 TYR B 11 -35.05 70.41 REMARK 500 PHE B 79 -12.53 72.88 REMARK 500 LYS B 169 105.05 29.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JX0 RELATED DB: PDB REMARK 900 RELATED ID: 5JX3 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 WESTERN RESERVE (WR109) VACCINIA VIRUS STRAIN WAS USED. THE CLOSEST REMARK 999 SEQUENCE DATABASE ENTRY IS: AA089388. ANY SEQUENCE DIFFERENCE FROM REMARK 999 THIS ENTRY EXCEPT FOR THE ENGINEERED MUTATIONS IN THE D4 MUTANTS IS REMARK 999 UNINTENTIONAL DBREF 5JX8 A 1 218 UNP P04303 UNG_VACCW 1 218 DBREF 5JX8 B 1 218 UNP P04303 UNG_VACCW 1 218 SEQADV 5JX8 MET A -19 UNP P04303 INITIATING METHIONINE SEQADV 5JX8 GLY A -18 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER A -17 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER A -16 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -15 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -14 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -13 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -12 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -11 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A -10 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER A -9 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER A -8 UNP P04303 EXPRESSION TAG SEQADV 5JX8 GLY A -7 UNP P04303 EXPRESSION TAG SEQADV 5JX8 LEU A -6 UNP P04303 EXPRESSION TAG SEQADV 5JX8 VAL A -5 UNP P04303 EXPRESSION TAG SEQADV 5JX8 PRO A -4 UNP P04303 EXPRESSION TAG SEQADV 5JX8 ARG A -3 UNP P04303 EXPRESSION TAG SEQADV 5JX8 GLY A -2 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER A -1 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS A 0 UNP P04303 EXPRESSION TAG SEQADV 5JX8 ASN A 17 UNP P04303 ASP 17 SEE REMARK 999 SEQADV 5JX8 PHE A 163 UNP P04303 TYR 163 SEE REMARK 999 SEQADV 5JX8 MET B -19 UNP P04303 INITIATING METHIONINE SEQADV 5JX8 GLY B -18 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER B -17 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER B -16 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -15 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -14 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -13 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -12 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -11 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B -10 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER B -9 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER B -8 UNP P04303 EXPRESSION TAG SEQADV 5JX8 GLY B -7 UNP P04303 EXPRESSION TAG SEQADV 5JX8 LEU B -6 UNP P04303 EXPRESSION TAG SEQADV 5JX8 VAL B -5 UNP P04303 EXPRESSION TAG SEQADV 5JX8 PRO B -4 UNP P04303 EXPRESSION TAG SEQADV 5JX8 ARG B -3 UNP P04303 EXPRESSION TAG SEQADV 5JX8 GLY B -2 UNP P04303 EXPRESSION TAG SEQADV 5JX8 SER B -1 UNP P04303 EXPRESSION TAG SEQADV 5JX8 HIS B 0 UNP P04303 EXPRESSION TAG SEQADV 5JX8 ASN B 17 UNP P04303 ASP 17 SEE REMARK 999 SEQADV 5JX8 PHE B 163 UNP P04303 TYR 163 SEE REMARK 999 SEQRES 1 A 238 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 238 LEU VAL PRO ARG GLY SER HIS MET ASN SER VAL THR VAL SEQRES 3 A 238 SER HIS ALA PRO TYR THR ILE THR TYR HIS ASN ASP TRP SEQRES 4 A 238 GLU PRO VAL MET SER GLN LEU VAL GLU PHE TYR ASN GLU SEQRES 5 A 238 VAL ALA SER TRP LEU LEU ARG ASP GLU THR SER PRO ILE SEQRES 6 A 238 PRO ASP LYS PHE PHE ILE GLN LEU LYS GLN PRO LEU ARG SEQRES 7 A 238 ASN LYS ARG VAL CYS VAL CYS GLY ILE ASP PRO TYR PRO SEQRES 8 A 238 LYS ASP GLY THR GLY VAL PRO PHE GLU SER PRO ASN PHE SEQRES 9 A 238 THR LYS LYS SER ILE LYS GLU ILE ALA SER SER ILE SER SEQRES 10 A 238 ARG LEU THR GLY VAL ILE ASP TYR LYS GLY TYR ASN LEU SEQRES 11 A 238 ASN ILE ILE ASP GLY VAL ILE PRO TRP ASN TYR TYR LEU SEQRES 12 A 238 SER CYS LYS LEU GLY GLU THR LYS SER HIS ALA ILE TYR SEQRES 13 A 238 TRP ASP LYS ILE SER LYS LEU LEU LEU GLN HIS ILE THR SEQRES 14 A 238 LYS HIS VAL SER VAL LEU TYR CYS LEU GLY LYS THR ASP SEQRES 15 A 238 PHE SER ASN ILE ARG ALA LYS LEU GLU SER PRO VAL THR SEQRES 16 A 238 THR ILE VAL GLY TYR HIS PRO ALA ALA ARG ASP ARG GLN SEQRES 17 A 238 PHE GLU LYS ASP ARG SER PHE GLU ILE ILE ASN VAL LEU SEQRES 18 A 238 LEU GLU LEU ASP ASN LYS ALA PRO ILE ASN TRP ALA GLN SEQRES 19 A 238 GLY PHE ILE TYR SEQRES 1 B 238 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 238 LEU VAL PRO ARG GLY SER HIS MET ASN SER VAL THR VAL SEQRES 3 B 238 SER HIS ALA PRO TYR THR ILE THR TYR HIS ASN ASP TRP SEQRES 4 B 238 GLU PRO VAL MET SER GLN LEU VAL GLU PHE TYR ASN GLU SEQRES 5 B 238 VAL ALA SER TRP LEU LEU ARG ASP GLU THR SER PRO ILE SEQRES 6 B 238 PRO ASP LYS PHE PHE ILE GLN LEU LYS GLN PRO LEU ARG SEQRES 7 B 238 ASN LYS ARG VAL CYS VAL CYS GLY ILE ASP PRO TYR PRO SEQRES 8 B 238 LYS ASP GLY THR GLY VAL PRO PHE GLU SER PRO ASN PHE SEQRES 9 B 238 THR LYS LYS SER ILE LYS GLU ILE ALA SER SER ILE SER SEQRES 10 B 238 ARG LEU THR GLY VAL ILE ASP TYR LYS GLY TYR ASN LEU SEQRES 11 B 238 ASN ILE ILE ASP GLY VAL ILE PRO TRP ASN TYR TYR LEU SEQRES 12 B 238 SER CYS LYS LEU GLY GLU THR LYS SER HIS ALA ILE TYR SEQRES 13 B 238 TRP ASP LYS ILE SER LYS LEU LEU LEU GLN HIS ILE THR SEQRES 14 B 238 LYS HIS VAL SER VAL LEU TYR CYS LEU GLY LYS THR ASP SEQRES 15 B 238 PHE SER ASN ILE ARG ALA LYS LEU GLU SER PRO VAL THR SEQRES 16 B 238 THR ILE VAL GLY TYR HIS PRO ALA ALA ARG ASP ARG GLN SEQRES 17 B 238 PHE GLU LYS ASP ARG SER PHE GLU ILE ILE ASN VAL LEU SEQRES 18 B 238 LEU GLU LEU ASP ASN LYS ALA PRO ILE ASN TRP ALA GLN SEQRES 19 B 238 GLY PHE ILE TYR HET SO4 A 301 5 HET SO4 A 302 5 HET GOL A 303 6 HET GOL A 304 6 HET SO4 B 301 5 HET GOL B 302 6 HET GOL B 303 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 3(O4 S 2-) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 10 HOH *150(H2 O) HELIX 1 AA1 TRP A 19 ARG A 39 1 21 HELIX 2 AA2 ILE A 45 PHE A 49 5 5 HELIX 3 AA3 PHE A 50 GLN A 55 5 6 HELIX 4 AA4 LYS A 86 GLY A 101 1 16 HELIX 5 AA5 LEU A 110 ILE A 113 5 4 HELIX 6 AA6 HIS A 133 LYS A 150 1 18 HELIX 7 AA7 ARG A 187 ASP A 205 1 19 HELIX 8 AA8 ASN A 211 GLN A 214 5 4 HELIX 9 AA9 TRP B 19 LEU B 38 1 20 HELIX 10 AB1 ILE B 45 PHE B 49 5 5 HELIX 11 AB2 PHE B 50 GLN B 55 5 6 HELIX 12 AB3 LYS B 86 GLY B 101 1 16 HELIX 13 AB4 LEU B 110 ILE B 113 5 4 HELIX 14 AB5 HIS B 133 VAL B 152 1 20 HELIX 15 AB6 ARG B 187 ASP B 205 1 19 HELIX 16 AB7 ASN B 211 GLN B 214 5 4 SHEET 1 AA1 2 MET A 1 THR A 5 0 SHEET 2 AA1 2 THR A 12 HIS A 16 -1 O ILE A 13 N VAL A 4 SHEET 1 AA2 2 THR A 42 SER A 43 0 SHEET 2 AA2 2 CYS A 125 LYS A 126 -1 O CYS A 125 N SER A 43 SHEET 1 AA3 4 VAL A 116 ASN A 120 0 SHEET 2 AA3 4 VAL A 62 GLY A 66 1 N VAL A 64 O TRP A 119 SHEET 3 AA3 4 VAL A 154 LEU A 158 1 O TYR A 156 N CYS A 65 SHEET 4 AA3 4 THR A 175 GLY A 179 1 O GLY A 179 N CYS A 157 SHEET 1 AA4 2 GLY A 107 TYR A 108 0 SHEET 2 AA4 2 PHE A 216 ILE A 217 -1 O ILE A 217 N GLY A 107 SHEET 1 AA5 2 MET B 1 THR B 5 0 SHEET 2 AA5 2 THR B 12 HIS B 16 -1 O TYR B 15 N ASN B 2 SHEET 1 AA6 2 THR B 42 SER B 43 0 SHEET 2 AA6 2 CYS B 125 LYS B 126 -1 O CYS B 125 N SER B 43 SHEET 1 AA7 4 GLY B 115 ASN B 120 0 SHEET 2 AA7 4 LYS B 60 GLY B 66 1 N ARG B 61 O GLY B 115 SHEET 3 AA7 4 VAL B 154 LEU B 158 1 O TYR B 156 N CYS B 63 SHEET 4 AA7 4 THR B 175 GLY B 179 1 O GLY B 179 N CYS B 157 SHEET 1 AA8 2 GLY B 107 TYR B 108 0 SHEET 2 AA8 2 PHE B 216 ILE B 217 -1 O ILE B 217 N GLY B 107 CISPEP 1 ALA A 9 PRO A 10 0 6.06 CISPEP 2 SER A 43 PRO A 44 0 -6.84 CISPEP 3 ALA B 9 PRO B 10 0 4.90 CISPEP 4 SER B 43 PRO B 44 0 -5.02 SITE 1 AC1 6 LYS A 160 THR A 161 TYR A 180 HIS A 181 SITE 2 AC1 6 HOH A 459 HOH A 476 SITE 1 AC2 5 VAL A 4 THR A 5 HOH A 426 HOH A 432 SITE 2 AC2 5 ILE B 112 SITE 1 AC3 6 GLY A -2 PRO A -4 ARG A -3 SER A -1 SITE 2 AC3 6 HIS A 0 HOH A 409 SITE 1 AC4 8 ASP A 68 PRO A 69 TYR A 70 PRO A 78 SITE 2 AC4 8 PHE A 79 ASN A 120 HOH A 421 HOH A 452 SITE 1 AC5 5 LYS B 160 THR B 161 TYR B 180 HIS B 181 SITE 2 AC5 5 HOH B 441 SITE 1 AC6 5 ASP B 68 PRO B 69 TYR B 70 PHE B 79 SITE 2 AC6 5 ASN B 120 SITE 1 AC7 2 LYS B 87 HOH B 448 CRYST1 85.130 85.130 139.050 90.00 90.00 120.00 P 32 2 1 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 0.011747 0.006782 0.000000 0.00000 SCALE2 0.000000 0.013564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007192 0.00000