HEADER HYDROLASE/DNA 10-SEP-20 7K30 TITLE CRYSTAL STRUCTURE OF ENDONUCLEASE Q COMPLEX WITH 27-MER DUPLEX TITLE 2 SUBSTRATE WITH DU AT THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE Q; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (27-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (27-MER); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, DEAMINATION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,N.M.MOELLER,S.BANERJEE,L.YIN,K.ORELLANA,H.AIHARA REVDAT 2 18-OCT-23 7K30 1 REMARK REVDAT 1 17-MAR-21 7K30 0 JRNL AUTH K.SHI,N.H.MOELLER,S.BANERJEE,J.L.MCCANN,M.A.CARPENTER,L.YIN, JRNL AUTH 2 R.MOORTHY,K.ORELLANA,D.A.HARKI,R.S.HARRIS,H.AIHARA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF DISTINCT DEAMINATED DNA JRNL TITL 2 LESIONS BY ENDONUCLEASE Q. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33658373 JRNL DOI 10.1073/PNAS.2021120118 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 65.5 REMARK 3 NUMBER OF REFLECTIONS : 28591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1411 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 88.1200 - 5.0300 1.00 4108 237 0.1521 0.1822 REMARK 3 2 5.0300 - 3.9900 1.00 4135 241 0.1499 0.1685 REMARK 3 3 3.9900 - 3.4900 1.00 4155 203 0.1983 0.2357 REMARK 3 4 3.4900 - 3.1700 1.00 4129 202 0.2365 0.2708 REMARK 3 5 3.1700 - 2.9400 1.00 4175 198 0.2930 0.3231 REMARK 3 6 2.9400 - 2.7700 0.79 3277 144 0.3410 0.3921 REMARK 3 7 2.7700 - 2.6300 0.40 1644 102 0.3488 0.3503 REMARK 3 8 2.6300 - 2.5200 0.24 968 58 0.3794 0.3391 REMARK 3 9 2.5200 - 2.4200 0.11 468 19 0.5674 0.6917 REMARK 3 10 2.4200 - 2.3400 0.03 121 7 1.1200 0.4503 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.52 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9862 25.4739 -17.4449 REMARK 3 T TENSOR REMARK 3 T11: 0.5317 T22: 0.3235 REMARK 3 T33: -0.1269 T12: -0.0875 REMARK 3 T13: 0.2185 T23: 0.0829 REMARK 3 L TENSOR REMARK 3 L11: 0.2714 L22: 0.6989 REMARK 3 L33: 0.9378 L12: 0.0648 REMARK 3 L13: 0.0605 L23: -0.2612 REMARK 3 S TENSOR REMARK 3 S11: -0.1958 S12: -0.1955 S13: -0.2202 REMARK 3 S21: 0.1583 S22: 0.1249 S23: 0.0683 REMARK 3 S31: 0.6697 S32: -0.1156 S33: 0.0745 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2537 31.1612 -26.6581 REMARK 3 T TENSOR REMARK 3 T11: 0.2194 T22: 0.5414 REMARK 3 T33: -0.1763 T12: -0.1249 REMARK 3 T13: 0.2508 T23: 0.0507 REMARK 3 L TENSOR REMARK 3 L11: 0.6059 L22: 0.7636 REMARK 3 L33: 1.9683 L12: -0.2879 REMARK 3 L13: 0.1334 L23: 0.1783 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: -0.1936 S13: -0.1975 REMARK 3 S21: 0.1184 S22: 0.0465 S23: 0.2593 REMARK 3 S31: 0.5025 S32: -0.5858 S33: 0.1187 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 106 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4057 32.7848 -37.4220 REMARK 3 T TENSOR REMARK 3 T11: 0.2361 T22: 0.3509 REMARK 3 T33: 0.0267 T12: -0.1244 REMARK 3 T13: -0.0734 T23: -0.0731 REMARK 3 L TENSOR REMARK 3 L11: 1.4412 L22: 1.8569 REMARK 3 L33: 4.3786 L12: -0.3786 REMARK 3 L13: -0.5815 L23: 0.0702 REMARK 3 S TENSOR REMARK 3 S11: -0.2197 S12: 0.1951 S13: -0.0760 REMARK 3 S21: -0.2132 S22: -0.1157 S23: 0.2391 REMARK 3 S31: 0.5982 S32: -0.2952 S33: -0.0937 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.4276 36.2483 -26.5151 REMARK 3 T TENSOR REMARK 3 T11: 0.0450 T22: 0.4366 REMARK 3 T33: 0.1264 T12: 0.1312 REMARK 3 T13: -0.0147 T23: 0.1226 REMARK 3 L TENSOR REMARK 3 L11: 1.9723 L22: 0.7903 REMARK 3 L33: 1.8303 L12: -0.2407 REMARK 3 L13: 0.0425 L23: 0.1677 REMARK 3 S TENSOR REMARK 3 S11: -0.4001 S12: 0.3988 S13: 0.0117 REMARK 3 S21: 0.0643 S22: -0.0508 S23: -0.2311 REMARK 3 S31: 0.2151 S32: 0.4329 S33: -0.2249 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 278 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.8770 32.0510 -23.1693 REMARK 3 T TENSOR REMARK 3 T11: 0.4049 T22: 0.6731 REMARK 3 T33: 0.1245 T12: 0.3769 REMARK 3 T13: 0.0939 T23: 0.0984 REMARK 3 L TENSOR REMARK 3 L11: 1.1899 L22: 1.2183 REMARK 3 L33: 1.7693 L12: 0.1064 REMARK 3 L13: -0.0424 L23: 0.2831 REMARK 3 S TENSOR REMARK 3 S11: -0.1238 S12: 0.4018 S13: -0.1745 REMARK 3 S21: -0.2812 S22: -0.2323 S23: -0.4412 REMARK 3 S31: 0.3208 S32: 0.3556 S33: -0.1645 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 279 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.6361 43.0566 -24.0468 REMARK 3 T TENSOR REMARK 3 T11: 0.1642 T22: 0.7296 REMARK 3 T33: 0.5171 T12: 0.0414 REMARK 3 T13: -0.0839 T23: 0.2061 REMARK 3 L TENSOR REMARK 3 L11: 2.5416 L22: 1.3202 REMARK 3 L33: 0.9709 L12: -0.4702 REMARK 3 L13: -0.4179 L23: 0.5631 REMARK 3 S TENSOR REMARK 3 S11: -0.1194 S12: 0.7437 S13: 0.5762 REMARK 3 S21: -0.0911 S22: 0.1445 S23: -0.6143 REMARK 3 S31: -0.0510 S32: 0.7184 S33: -0.0252 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 299 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.0751 20.0189 -4.6239 REMARK 3 T TENSOR REMARK 3 T11: 0.8009 T22: 0.2986 REMARK 3 T33: 0.2524 T12: 0.2080 REMARK 3 T13: -0.0473 T23: 0.1821 REMARK 3 L TENSOR REMARK 3 L11: 0.8494 L22: 2.4345 REMARK 3 L33: 0.9195 L12: -0.3300 REMARK 3 L13: -0.0726 L23: -0.9662 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: -0.3079 S13: -0.5253 REMARK 3 S21: 0.0732 S22: 0.1751 S23: 0.2570 REMARK 3 S31: 1.0174 S32: 0.0741 S33: -0.2863 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.4487 25.2915 -2.3745 REMARK 3 T TENSOR REMARK 3 T11: 0.6960 T22: 0.7195 REMARK 3 T33: 0.3055 T12: 0.6025 REMARK 3 T13: -0.0830 T23: 0.1522 REMARK 3 L TENSOR REMARK 3 L11: 0.9521 L22: 1.8008 REMARK 3 L33: 0.2235 L12: 0.5363 REMARK 3 L13: -0.3223 L23: 0.2136 REMARK 3 S TENSOR REMARK 3 S11: 0.1245 S12: -0.2876 S13: -0.3011 REMARK 3 S21: 0.2766 S22: -0.0653 S23: -0.6800 REMARK 3 S31: 0.4484 S32: 0.6737 S33: 0.1995 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.0973 -2.5016 -7.3361 REMARK 3 T TENSOR REMARK 3 T11: 2.3829 T22: 0.8340 REMARK 3 T33: 0.9290 T12: 0.2425 REMARK 3 T13: -0.1035 T23: 0.2995 REMARK 3 L TENSOR REMARK 3 L11: 5.4482 L22: 6.9401 REMARK 3 L33: 2.7283 L12: -0.3054 REMARK 3 L13: 0.5115 L23: -4.3339 REMARK 3 S TENSOR REMARK 3 S11: -0.0065 S12: -0.1041 S13: -0.7388 REMARK 3 S21: -0.7223 S22: 0.2206 S23: 0.5013 REMARK 3 S31: 1.4223 S32: -0.1372 S33: -0.0974 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.9329 8.5112 -31.1572 REMARK 3 T TENSOR REMARK 3 T11: 1.8831 T22: 1.0237 REMARK 3 T33: 0.9155 T12: 0.1481 REMARK 3 T13: -0.1388 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 3.7797 L22: 5.2967 REMARK 3 L33: 4.8467 L12: -4.0990 REMARK 3 L13: 4.1769 L23: -4.9729 REMARK 3 S TENSOR REMARK 3 S11: 0.2447 S12: 1.1386 S13: -0.9866 REMARK 3 S21: -0.0175 S22: 0.3381 S23: 0.5921 REMARK 3 S31: 1.5167 S32: 0.9577 S33: -0.6061 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 17 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9310 16.2292 -54.1905 REMARK 3 T TENSOR REMARK 3 T11: 1.6515 T22: 2.0316 REMARK 3 T33: 1.0639 T12: 0.2406 REMARK 3 T13: 0.7068 T23: -0.3793 REMARK 3 L TENSOR REMARK 3 L11: 0.1221 L22: 0.5822 REMARK 3 L33: 0.0078 L12: 0.2623 REMARK 3 L13: 0.0298 L23: 0.0697 REMARK 3 S TENSOR REMARK 3 S11: 0.1191 S12: 1.0083 S13: 0.0232 REMARK 3 S21: -0.8545 S22: 0.1812 S23: -0.5954 REMARK 3 S31: 0.8693 S32: 0.2415 S33: 0.0369 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.6058 15.7916 -56.0459 REMARK 3 T TENSOR REMARK 3 T11: 2.1498 T22: 2.0817 REMARK 3 T33: 1.1290 T12: 0.2545 REMARK 3 T13: 0.7713 T23: -0.4247 REMARK 3 L TENSOR REMARK 3 L11: 0.2345 L22: 0.9886 REMARK 3 L33: 0.9785 L12: 0.4239 REMARK 3 L13: -0.2719 L23: -0.8736 REMARK 3 S TENSOR REMARK 3 S11: 0.0772 S12: 0.9310 S13: -0.0812 REMARK 3 S21: 0.2309 S22: 0.0845 S23: -0.1658 REMARK 3 S31: 0.3686 S32: -0.4650 S33: -0.4573 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2266 5.8225 -16.3578 REMARK 3 T TENSOR REMARK 3 T11: 1.8347 T22: 0.6700 REMARK 3 T33: 0.6725 T12: 0.2676 REMARK 3 T13: -0.0114 T23: 0.1209 REMARK 3 L TENSOR REMARK 3 L11: 1.9099 L22: 0.1388 REMARK 3 L33: 0.1573 L12: -0.5236 REMARK 3 L13: 0.5507 L23: -0.1513 REMARK 3 S TENSOR REMARK 3 S11: 0.5162 S12: -0.2584 S13: -0.8663 REMARK 3 S21: -0.0391 S22: -0.0902 S23: 0.0996 REMARK 3 S31: 1.6702 S32: 0.5473 S33: -0.2414 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 7K30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44238 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 88.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 9.90000 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: PHASER REMARK 200 STARTING MODEL: 5ZB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-POTASSIUM CITRATE AND 15 % REMARK 280 (W/V) POLYETHYLENE GLYCOL (PEG) 3,350, PH 7.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 76.35000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.08069 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.39000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 76.35000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 44.08069 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.39000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 76.35000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 44.08069 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.39000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 88.16139 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 78.78000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 88.16139 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 78.78000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 88.16139 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 78.78000 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: 6680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 SER A 396 REMARK 465 ILE A 397 REMARK 465 GLU A 398 REMARK 465 ILE A 399 REMARK 465 SER A 400 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 O2 DC C 7 O HOH C 101 2.17 REMARK 500 OG1 THR A 91 OE1 GLN A 94 2.18 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. = 2.1 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG C 19 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 19 O4' - C1' - N9 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 ASP A 60 -159.19 -147.19 REMARK 500 HIS A 139 59.13 36.94 REMARK 500 MET A 179 8.03 -66.24 REMARK 500 ARG A 201 -68.05 -108.26 REMARK 500 ARG A 251 -60.66 -108.59 REMARK 500 ASP A 288 -47.72 -132.14 REMARK 500 ASP A 295 3.57 -69.99 REMARK 500 ASN A 365 14.34 58.37 REMARK 500 LYS A 366 34.79 -93.42 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE1 REMARK 620 2 GLU A 76 OE2 60.9 REMARK 620 3 HIS A 84 ND1 109.7 115.2 REMARK 620 4 HIS A 139 NE2 148.5 89.7 92.1 REMARK 620 5 DU C 14 OP2 74.5 132.4 93.7 128.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 169 O REMARK 620 2 LEU A 170 O 72.1 REMARK 620 3 ALA A 172 O 64.1 88.1 REMARK 620 4 GLU A 205 OE2 89.7 102.0 147.7 REMARK 620 5 LEU A 237 O 153.9 81.9 113.9 98.0 REMARK 620 6 TYR A 299 OH 120.6 159.2 84.0 94.8 83.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 249 SG REMARK 620 2 CYS A 252 SG 112.7 REMARK 620 3 CYS A 268 SG 123.2 98.0 REMARK 620 4 CYS A 271 SG 94.9 100.4 126.0 REMARK 620 N 1 2 3 DBREF 7K30 A 1 400 UNP I6V2I0 I6V2I0_9EURY 1 400 DBREF 7K30 B 1 27 PDB 7K30 7K30 1 27 DBREF 7K30 C 1 27 PDB 7K30 7K30 1 27 SEQADV 7K30 ASN A 193 UNP I6V2I0 ASP 193 ENGINEERED MUTATION SEQRES 1 A 400 MET ILE VAL ASP GLY ASP LEU HIS ILE HIS SER HIS TYR SEQRES 2 A 400 SER LYS ALA VAL SER LYS LEU MET THR PHE PRO ILE ILE SEQRES 3 A 400 ALA GLU ASN ALA LYS LEU LYS GLY LEU ASN LEU VAL GLY SEQRES 4 A 400 THR GLY ASP SER LEU ASN PRO HIS TRP GLU LYS GLU LEU SEQRES 5 A 400 LEU LYS HIS SER LYS PRO ILE ASP ASP GLY THR PHE GLU SEQRES 6 A 400 VAL ASN GLY VAL LYS PHE ILE LEU THR CYS GLU VAL GLU SEQRES 7 A 400 ASP LYS ARG ARG VAL HIS HIS LEU LEU ILE PHE PRO THR SEQRES 8 A 400 LEU SER GLN VAL ARG GLU PHE ARG GLU LYS VAL LYS ILE SEQRES 9 A 400 TYR SER THR ASN ILE GLU SER GLU GLY ARG PRO ASN LEU SEQRES 10 A 400 ASN LEU THR ALA GLU GLU ILE ALA GLU MET ALA ASN GLU SEQRES 11 A 400 LEU ASP ILE LEU ILE GLY PRO ALA HIS ALA PHE THR PRO SEQRES 12 A 400 TRP THR SER LEU TYR LYS GLU TYR ASP SER LEU LYS ASP SEQRES 13 A 400 ALA TYR GLY ASP ALA LYS ILE ASP PHE LEU GLU LEU GLY SEQRES 14 A 400 LEU SER ALA ASP SER ASP MET ALA ASP MET ILE LYS ALA SEQRES 15 A 400 HIS HIS SER ILE PRO TYR LEU SER ASN SER ASN ALA HIS SEQRES 16 A 400 SER PRO ASN PRO HIS ARG LEU GLY ARG GLU PHE ASN ARG SEQRES 17 A 400 PHE GLU VAL LYS ASP VAL THR PHE GLU GLU ILE ARG LYS SEQRES 18 A 400 ALA ILE LYS GLY VAL GLY GLY ARG LYS ILE MET LEU ASN SEQRES 19 A 400 ALA GLY LEU ASP PRO ARG LEU GLY LYS TYR HIS LEU THR SEQRES 20 A 400 ALA CYS SER ARG CYS TYR THR LYS TYR THR LEU GLN ASP SEQRES 21 A 400 ALA VAL SER LEU SER TRP LYS CYS PRO LYS CYS GLY GLY SEQRES 22 A 400 ILE ILE LYS LYS GLY VAL ARG ASP ARG ILE LEU GLU LEU SEQRES 23 A 400 ALA ASP THR SER GLU LYS PRO LYS ASP ARG PRO PRO TYR SEQRES 24 A 400 VAL ARG LEU ALA PRO LEU ALA GLU ILE ILE ALA MET VAL SEQRES 25 A 400 LEU GLY LYS GLY ILE GLU SER LYS ALA VAL LYS LEU LEU SEQRES 26 A 400 TRP ASN ARG PHE LEU ARG GLU PHE GLY SER GLU ILE ARG SEQRES 27 A 400 VAL LEU ILE ASP LEU PRO ILE GLU SER ILE ALA SER VAL SEQRES 28 A 400 HIS GLU GLY VAL ALA LYS ALA ILE TRP ALA TYR ARG ASN SEQRES 29 A 400 ASN LYS LEU ILE ILE VAL PRO GLY GLY GLY GLY LYS TYR SEQRES 30 A 400 GLY GLU ILE ARG ILE PRO GLU GLU ILE LEU LYS ALA LYS SEQRES 31 A 400 ILE GLU ASP LEU ASN SER ILE GLU ILE SER SEQRES 1 B 27 DG DT DC DG DT DT DC DG DC DT DA DC DA SEQRES 2 B 27 DG DG BRU DC DG DT DC DG DG DT DC DT DG SEQRES 3 B 27 DC SEQRES 1 C 27 DG DC DA DG DA DC DC DG DA DC DG DA DC SEQRES 2 C 27 DU DT DG DT DA DG DC DG DA DA DC DG DA SEQRES 3 C 27 DC HET BRU B 16 20 HET ZN A 501 1 HET ZN A 502 1 HET MG A 503 1 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 BRU C9 H12 BR N2 O8 P FORMUL 4 ZN 2(ZN 2+) FORMUL 6 MG MG 2+ FORMUL 7 EDO 4(C2 H6 O2) FORMUL 11 HOH *55(H2 O) HELIX 1 AA1 THR A 22 GLY A 34 1 13 HELIX 2 AA2 ASN A 45 SER A 56 1 12 HELIX 3 AA3 THR A 91 LYS A 103 1 13 HELIX 4 AA4 ILE A 104 SER A 106 5 3 HELIX 5 AA5 THR A 120 LEU A 131 1 12 HELIX 6 AA6 SER A 153 GLY A 159 1 7 HELIX 7 AA7 ASP A 173 MET A 179 1 7 HELIX 8 AA8 ILE A 180 ILE A 186 5 7 HELIX 9 AA9 THR A 215 GLY A 225 1 11 HELIX 10 AB1 PRO A 239 GLY A 242 5 4 HELIX 11 AB2 THR A 257 SER A 265 1 9 HELIX 12 AB3 GLY A 278 LEU A 286 1 9 HELIX 13 AB4 PRO A 304 GLY A 314 1 11 HELIX 14 AB5 SER A 319 GLY A 334 1 16 HELIX 15 AB6 SER A 335 ILE A 341 1 7 HELIX 16 AB7 PRO A 344 HIS A 352 1 9 HELIX 17 AB8 HIS A 352 ASN A 364 1 13 HELIX 18 AB9 PRO A 383 ALA A 389 1 7 SHEET 1 AA1 5 LYS A 57 PRO A 58 0 SHEET 2 AA1 5 THR A 63 VAL A 66 -1 O GLU A 65 N LYS A 57 SHEET 3 AA1 5 VAL A 69 GLU A 78 -1 O VAL A 69 N VAL A 66 SHEET 4 AA1 5 HIS A 84 PHE A 89 -1 O LEU A 87 N CYS A 75 SHEET 5 AA1 5 LEU A 134 PRO A 137 -1 O GLY A 136 N LEU A 86 SHEET 1 AA2 8 LYS A 57 PRO A 58 0 SHEET 2 AA2 8 THR A 63 VAL A 66 -1 O GLU A 65 N LYS A 57 SHEET 3 AA2 8 VAL A 69 GLU A 78 -1 O VAL A 69 N VAL A 66 SHEET 4 AA2 8 LEU A 37 GLY A 39 1 N VAL A 38 O LYS A 70 SHEET 5 AA2 8 ILE A 2 ASP A 6 1 N ASP A 6 O GLY A 39 SHEET 6 AA2 8 PHE A 206 GLU A 210 -1 O ASN A 207 N GLY A 5 SHEET 7 AA2 8 LYS A 230 LEU A 237 -1 O ALA A 235 N PHE A 206 SHEET 8 AA2 8 TYR A 299 LEU A 302 1 O LEU A 302 N GLY A 236 SHEET 1 AA3 2 LEU A 166 GLU A 167 0 SHEET 2 AA3 2 TYR A 188 LEU A 189 1 O LEU A 189 N LEU A 166 SHEET 1 AA4 2 ALA A 248 CYS A 249 0 SHEET 2 AA4 2 ILE A 275 LYS A 276 -1 O LYS A 276 N ALA A 248 SHEET 1 AA5 2 ILE A 368 VAL A 370 0 SHEET 2 AA5 2 GLU A 379 ARG A 381 -1 O ARG A 381 N ILE A 368 LINK O3' DG B 15 P BRU B 16 1555 1555 1.61 LINK O3' BRU B 16 P DC B 17 1555 1555 1.61 LINK OE1 GLU A 76 ZN ZN A 501 1555 1555 2.16 LINK OE2 GLU A 76 ZN ZN A 501 1555 1555 2.12 LINK ND1 HIS A 84 ZN ZN A 501 1555 1555 2.02 LINK NE2 HIS A 139 ZN ZN A 501 1555 1555 2.09 LINK O GLY A 169 MG MG A 503 1555 1555 2.70 LINK O LEU A 170 MG MG A 503 1555 1555 2.67 LINK O ALA A 172 MG MG A 503 1555 1555 2.64 LINK OE2 GLU A 205 MG MG A 503 1555 1555 2.24 LINK O LEU A 237 MG MG A 503 1555 1555 2.81 LINK SG CYS A 249 ZN ZN A 502 1555 1555 2.30 LINK SG CYS A 252 ZN ZN A 502 1555 1555 2.25 LINK SG CYS A 268 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 271 ZN ZN A 502 1555 1555 2.27 LINK OH TYR A 299 MG MG A 503 1555 1555 2.19 LINK ZN ZN A 501 OP2 DU C 14 1555 1555 2.16 CRYST1 152.700 152.700 118.170 90.00 90.00 120.00 H 3 9 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 0.006549 0.003781 0.000000 0.00000 SCALE2 0.000000 0.007562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008462 0.00000