HEADER HYDROLASE 28-APR-13 4KG3 TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE DCP2 NUDIX DOMAIN IN TITLE 2 COMPLEX WITH MG (E153Q MUTATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA-DECAPPING ENZYME SUBUNIT 2; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: DCP2 NUDIX DOMAIN; COMPND 5 SYNONYM: PROTEIN PSU1; COMPND 6 EC: 3.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: DCP2, N1917, PSU1, YNL118C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-DUET1 KEYWDS NUDIX, MRNA DECAY, MRNA DECAPPING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.A.AGLIETTI,S.N.FLOOR,J.D.GROSS REVDAT 3 28-FEB-24 4KG3 1 REMARK SEQADV LINK REVDAT 2 25-SEP-13 4KG3 1 JRNL REVDAT 1 21-AUG-13 4KG3 0 JRNL AUTH R.A.AGLIETTI,S.N.FLOOR,C.L.MCCLENDON,M.P.JACOBSON,J.D.GROSS JRNL TITL ACTIVE SITE CONFORMATIONAL DYNAMICS ARE COUPLED TO CATALYSIS JRNL TITL 2 IN THE MRNA DECAPPING ENZYME DCP2. JRNL REF STRUCTURE V. 21 1571 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23911090 JRNL DOI 10.1016/J.STR.2013.06.021 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 54471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1713 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 46.5204 - 3.8937 0.98 5188 170 0.1519 0.1787 REMARK 3 2 3.8937 - 3.0907 0.98 5074 164 0.1664 0.2081 REMARK 3 3 3.0907 - 2.7001 0.97 4993 169 0.1766 0.2085 REMARK 3 4 2.7001 - 2.4532 0.95 4899 155 0.1811 0.2428 REMARK 3 5 2.4532 - 2.2774 0.94 4815 156 0.1707 0.2210 REMARK 3 6 2.2774 - 2.1431 0.93 4720 154 0.1732 0.1930 REMARK 3 7 2.1431 - 2.0358 0.90 4646 149 0.1755 0.2056 REMARK 3 8 2.0358 - 1.9472 0.85 4335 138 0.1927 0.2108 REMARK 3 9 1.9472 - 1.8722 0.77 3946 124 0.2033 0.2208 REMARK 3 10 1.8722 - 1.8076 0.72 3680 125 0.2458 0.3228 REMARK 3 11 1.8076 - 1.7511 0.67 3387 111 0.2906 0.3209 REMARK 3 12 1.7511 - 1.7000 0.60 3075 98 0.3545 0.4151 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.71 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 3639 REMARK 3 ANGLE : 1.110 4884 REMARK 3 CHIRALITY : 0.085 513 REMARK 3 PLANARITY : 0.004 627 REMARK 3 DIHEDRAL : 13.755 1405 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 102:131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.5108 31.2813 91.8506 REMARK 3 T TENSOR REMARK 3 T11: 0.1315 T22: 0.1485 REMARK 3 T33: 0.1545 T12: 0.0080 REMARK 3 T13: -0.0475 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 3.5333 L22: 4.7059 REMARK 3 L33: 2.7984 L12: 0.5785 REMARK 3 L13: 0.7770 L23: 0.5272 REMARK 3 S TENSOR REMARK 3 S11: -0.1465 S12: -0.0289 S13: 0.2273 REMARK 3 S21: 0.0444 S22: 0.1379 S23: 0.2306 REMARK 3 S31: -0.0417 S32: -0.2303 S33: -0.0074 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 132:192 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.4178 22.7857 89.5886 REMARK 3 T TENSOR REMARK 3 T11: 0.1895 T22: 0.1742 REMARK 3 T33: 0.1833 T12: -0.0139 REMARK 3 T13: -0.0455 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 3.3169 L22: 3.4845 REMARK 3 L33: 4.3405 L12: 0.3862 REMARK 3 L13: 0.4022 L23: -0.4485 REMARK 3 S TENSOR REMARK 3 S11: -0.0690 S12: 0.2665 S13: -0.2075 REMARK 3 S21: -0.2478 S22: 0.1534 S23: -0.0557 REMARK 3 S31: 0.2158 S32: -0.0296 S33: -0.1014 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 193:198 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.6634 30.4472 98.3740 REMARK 3 T TENSOR REMARK 3 T11: 0.1514 T22: 0.1594 REMARK 3 T33: 0.2454 T12: 0.0002 REMARK 3 T13: -0.0941 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 3.9337 L22: 3.7897 REMARK 3 L33: 3.4453 L12: 1.0949 REMARK 3 L13: -0.6420 L23: -2.4004 REMARK 3 S TENSOR REMARK 3 S11: -0.1575 S12: 0.1160 S13: -0.0565 REMARK 3 S21: -0.0059 S22: 0.2384 S23: -0.5521 REMARK 3 S31: -0.0776 S32: -0.0026 S33: 0.0176 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 199:223 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2505 39.0848 92.1007 REMARK 3 T TENSOR REMARK 3 T11: 0.2578 T22: 0.2698 REMARK 3 T33: 0.3625 T12: 0.0422 REMARK 3 T13: -0.1062 T23: 0.0268 REMARK 3 L TENSOR REMARK 3 L11: 2.4818 L22: 2.3282 REMARK 3 L33: 2.2725 L12: -2.0587 REMARK 3 L13: -0.2177 L23: -0.2932 REMARK 3 S TENSOR REMARK 3 S11: -0.2750 S12: 0.1466 S13: 0.4925 REMARK 3 S21: -0.0608 S22: 0.1786 S23: 0.2673 REMARK 3 S31: -0.5071 S32: -0.5176 S33: 0.0616 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 224:239 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4802 28.1120 85.6636 REMARK 3 T TENSOR REMARK 3 T11: 0.2570 T22: 0.3409 REMARK 3 T33: 0.4109 T12: 0.0173 REMARK 3 T13: -0.1227 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 6.3787 L22: 5.3338 REMARK 3 L33: 7.8922 L12: 0.2437 REMARK 3 L13: 0.2913 L23: -0.4454 REMARK 3 S TENSOR REMARK 3 S11: -0.2017 S12: 0.6564 S13: 0.2690 REMARK 3 S21: -0.4179 S22: -0.1190 S23: 1.0689 REMARK 3 S31: -0.3876 S32: -0.5624 S33: 0.0643 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESID 101:131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.1918 -0.6375 65.8897 REMARK 3 T TENSOR REMARK 3 T11: 0.1410 T22: 0.1542 REMARK 3 T33: 0.1056 T12: 0.0350 REMARK 3 T13: -0.0004 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 2.7131 L22: 2.8105 REMARK 3 L33: 5.2746 L12: -0.0095 REMARK 3 L13: 0.6833 L23: -0.1883 REMARK 3 S TENSOR REMARK 3 S11: 0.0699 S12: -0.0130 S13: 0.0258 REMARK 3 S21: -0.0066 S22: 0.0824 S23: 0.0737 REMARK 3 S31: -0.1036 S32: -0.1962 S33: -0.0431 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESID 132:192 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.4224 -9.3474 63.6362 REMARK 3 T TENSOR REMARK 3 T11: 0.1699 T22: 0.1807 REMARK 3 T33: 0.1474 T12: -0.0017 REMARK 3 T13: -0.0314 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 3.6878 L22: 2.7973 REMARK 3 L33: 3.5658 L12: 0.1156 REMARK 3 L13: 0.6858 L23: -0.1581 REMARK 3 S TENSOR REMARK 3 S11: 0.0501 S12: 0.1429 S13: -0.2438 REMARK 3 S21: -0.1854 S22: 0.1331 S23: 0.1607 REMARK 3 S31: 0.1939 S32: -0.2799 S33: -0.1062 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESID 193:213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.5527 3.1294 68.5978 REMARK 3 T TENSOR REMARK 3 T11: 0.2219 T22: 0.1183 REMARK 3 T33: 0.1407 T12: 0.0210 REMARK 3 T13: -0.0381 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 4.9844 L22: 2.2813 REMARK 3 L33: 5.9020 L12: -0.4935 REMARK 3 L13: -2.9642 L23: 0.8652 REMARK 3 S TENSOR REMARK 3 S11: -0.1153 S12: -0.3787 S13: 0.2509 REMARK 3 S21: 0.1919 S22: 0.1968 S23: -0.0487 REMARK 3 S31: -0.1388 S32: 0.2560 S33: -0.0891 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN B AND (RESID 214:227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.0741 8.8446 67.7425 REMARK 3 T TENSOR REMARK 3 T11: 0.3953 T22: 0.3033 REMARK 3 T33: 0.2879 T12: 0.1441 REMARK 3 T13: 0.0313 T23: 0.0968 REMARK 3 L TENSOR REMARK 3 L11: 5.5144 L22: 5.0194 REMARK 3 L33: 2.7267 L12: 1.8429 REMARK 3 L13: 1.1121 L23: 3.6908 REMARK 3 S TENSOR REMARK 3 S11: -0.0928 S12: -0.0484 S13: 0.6825 REMARK 3 S21: -0.3701 S22: 0.2929 S23: 0.7211 REMARK 3 S31: -0.7189 S32: -0.5023 S33: 0.1529 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN B AND (RESID 228:245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.8319 -7.3972 80.4863 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.2690 REMARK 3 T33: 0.1539 T12: 0.0301 REMARK 3 T13: 0.0320 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 3.0909 L22: 2.2073 REMARK 3 L33: 1.8775 L12: 1.7753 REMARK 3 L13: -0.0282 L23: 1.4769 REMARK 3 S TENSOR REMARK 3 S11: 0.3151 S12: -0.0332 S13: -0.0168 REMARK 3 S21: 0.5586 S22: -0.0173 S23: 0.3487 REMARK 3 S31: -0.2249 S32: -0.6533 S33: -0.0579 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN C AND (RESID 102:132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.5467 15.8130 37.1053 REMARK 3 T TENSOR REMARK 3 T11: 0.2700 T22: 0.2773 REMARK 3 T33: 0.1355 T12: 0.1066 REMARK 3 T13: -0.0006 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 4.2443 L22: 2.7813 REMARK 3 L33: 2.4350 L12: 0.2898 REMARK 3 L13: 0.4337 L23: 0.3772 REMARK 3 S TENSOR REMARK 3 S11: -0.0997 S12: -0.2300 S13: 0.0777 REMARK 3 S21: 0.2231 S22: 0.2916 S23: 0.1125 REMARK 3 S31: -0.4306 S32: -0.0660 S33: -0.0521 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN C AND (RESID 133:192 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.3622 7.2464 36.3587 REMARK 3 T TENSOR REMARK 3 T11: 0.2438 T22: 0.3436 REMARK 3 T33: 0.2370 T12: 0.0813 REMARK 3 T13: 0.0299 T23: 0.0974 REMARK 3 L TENSOR REMARK 3 L11: 1.4917 L22: 2.7277 REMARK 3 L33: 2.5226 L12: -0.1783 REMARK 3 L13: -0.3786 L23: 0.2248 REMARK 3 S TENSOR REMARK 3 S11: -0.2720 S12: -0.3608 S13: -0.2003 REMARK 3 S21: 0.1512 S22: 0.2776 S23: 0.5773 REMARK 3 S31: 0.1585 S32: -0.4657 S33: 0.0763 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN C AND (RESID 193:211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.4846 18.6528 33.3845 REMARK 3 T TENSOR REMARK 3 T11: 0.3827 T22: 0.1863 REMARK 3 T33: 0.2025 T12: 0.0442 REMARK 3 T13: -0.0508 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.7326 L22: 1.8562 REMARK 3 L33: 5.8152 L12: 0.8965 REMARK 3 L13: 0.7897 L23: 1.2958 REMARK 3 S TENSOR REMARK 3 S11: -0.1741 S12: -0.0568 S13: 0.3110 REMARK 3 S21: 0.2015 S22: 0.2411 S23: 0.0078 REMARK 3 S31: -0.5215 S32: 0.5450 S33: 0.0032 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN C AND (RESID 212:227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.8210 25.7952 43.4106 REMARK 3 T TENSOR REMARK 3 T11: 0.6681 T22: 0.4476 REMARK 3 T33: 0.3401 T12: 0.3076 REMARK 3 T13: 0.0165 T23: -0.0657 REMARK 3 L TENSOR REMARK 3 L11: 5.4501 L22: 0.2692 REMARK 3 L33: 5.1409 L12: 0.8543 REMARK 3 L13: -1.2259 L23: -1.0016 REMARK 3 S TENSOR REMARK 3 S11: -0.2105 S12: -0.8568 S13: 0.7542 REMARK 3 S21: 0.6565 S22: 0.2629 S23: 0.1664 REMARK 3 S31: -1.1289 S32: -0.1637 S33: -1.2813 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN C AND (RESID 228:245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.3128 9.1204 53.0554 REMARK 3 T TENSOR REMARK 3 T11: 0.5752 T22: 0.4456 REMARK 3 T33: 0.2057 T12: 0.1639 REMARK 3 T13: 0.0109 T23: 0.0419 REMARK 3 L TENSOR REMARK 3 L11: 2.8081 L22: 3.1757 REMARK 3 L33: 0.0813 L12: -0.8720 REMARK 3 L13: 0.4533 L23: -0.2886 REMARK 3 S TENSOR REMARK 3 S11: 0.1218 S12: -0.3194 S13: -0.1073 REMARK 3 S21: 0.3929 S22: -0.0428 S23: 0.3066 REMARK 3 S31: -0.9906 S32: -0.6071 S33: -0.0607 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 4KG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-11 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 19.7110 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.00000 REMARK 200 R SYM FOR SHELL (I) : 0.00000 REMARK 200 FOR SHELL : 0.684 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1 M MG FORMATE, 10 MM REMARK 280 HEPES, 1 MM DTT, 50 MM NACL, 100 MM NA2SO4, PH 7.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 70.39450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.39450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 503 LIES ON A SPECIAL POSITION. 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 LYS A 100 REMARK 465 LYS A 101 REMARK 465 GLN A 240 REMARK 465 ILE A 241 REMARK 465 LYS A 242 REMARK 465 ASN A 243 REMARK 465 GLU A 244 REMARK 465 ASP A 245 REMARK 465 LYS B 100 REMARK 465 LYS C 100 REMARK 465 LYS C 101 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 431 O HOH A 507 2.15 REMARK 500 O MET C 214 O HOH C 438 2.16 REMARK 500 OD2 ASP C 245 O HOH C 489 2.16 REMARK 500 O HOH B 430 O HOH B 463 2.18 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 LYS A 138 110.40 -173.66 REMARK 500 ASP A 139 -6.43 68.94 REMARK 500 LEU A 223 -49.68 71.94 REMARK 500 LYS B 138 -117.14 60.30 REMARK 500 LEU B 223 -52.44 71.48 REMARK 500 LYS C 216 -32.38 143.85 REMARK 500 LEU C 223 -56.22 74.01 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 149 OE1 REMARK 620 2 HOH A 401 O 85.7 REMARK 620 3 HOH A 406 O 92.3 89.0 REMARK 620 4 HOH A 408 O 90.4 176.1 90.5 REMARK 620 5 HOH A 412 O 174.1 90.7 82.9 93.0 REMARK 620 6 HOH A 513 O 93.9 90.8 173.7 90.1 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 149 OE1 REMARK 620 2 HOH B 403 O 91.4 REMARK 620 3 HOH B 406 O 86.5 87.3 REMARK 620 4 HOH C 402 O 90.9 170.6 83.7 REMARK 620 5 HOH C 404 O 91.4 95.0 176.9 94.1 REMARK 620 6 HOH C 532 O 177.2 88.1 96.3 90.0 85.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 149 OE1 REMARK 620 2 HOH C 416 O 92.6 REMARK 620 3 HOH C 419 O 90.8 172.8 REMARK 620 4 HOH C 434 O 174.4 90.0 87.1 REMARK 620 5 HOH C 486 O 93.5 83.0 90.5 91.7 REMARK 620 6 HOH C 533 O 86.9 90.8 95.6 88.2 173.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K6E RELATED DB: PDB REMARK 900 THE WILD-TYPE DOMAIN IN COMPLEX WITH MG REMARK 900 RELATED ID: 4KG4 RELATED DB: PDB DBREF 4KG3 A 100 245 UNP P53550 DCP2_YEAST 100 245 DBREF 4KG3 B 100 245 UNP P53550 DCP2_YEAST 100 245 DBREF 4KG3 C 100 245 UNP P53550 DCP2_YEAST 100 245 SEQADV 4KG3 GLN A 153 UNP P53550 GLU 153 ENGINEERED MUTATION SEQADV 4KG3 GLN B 153 UNP P53550 GLU 153 ENGINEERED MUTATION SEQADV 4KG3 GLN C 153 UNP P53550 GLU 153 ENGINEERED MUTATION SEQRES 1 A 146 LYS LYS SER ILE PRO VAL ARG GLY ALA ALA ILE PHE ASN SEQRES 2 A 146 GLU ASN LEU SER LYS ILE LEU LEU VAL GLN GLY THR GLU SEQRES 3 A 146 SER ASP SER TRP SER PHE PRO ARG GLY LYS ILE SER LYS SEQRES 4 A 146 ASP GLU ASN ASP ILE ASP CYS CYS ILE ARG GLU VAL LYS SEQRES 5 A 146 GLU GLN ILE GLY PHE ASP LEU THR ASP TYR ILE ASP ASP SEQRES 6 A 146 ASN GLN PHE ILE GLU ARG ASN ILE GLN GLY LYS ASN TYR SEQRES 7 A 146 LYS ILE PHE LEU ILE SER GLY VAL SER GLU VAL PHE ASN SEQRES 8 A 146 PHE LYS PRO GLN VAL ARG ASN GLU ILE ASP LYS ILE GLU SEQRES 9 A 146 TRP PHE ASP PHE LYS LYS ILE SER LYS THR MET TYR LYS SEQRES 10 A 146 SER ASN ILE LYS TYR TYR LEU ILE ASN SER MET MET ARG SEQRES 11 A 146 PRO LEU SER MET TRP LEU ARG HIS GLN ARG GLN ILE LYS SEQRES 12 A 146 ASN GLU ASP SEQRES 1 B 146 LYS LYS SER ILE PRO VAL ARG GLY ALA ALA ILE PHE ASN SEQRES 2 B 146 GLU ASN LEU SER LYS ILE LEU LEU VAL GLN GLY THR GLU SEQRES 3 B 146 SER ASP SER TRP SER PHE PRO ARG GLY LYS ILE SER LYS SEQRES 4 B 146 ASP GLU ASN ASP ILE ASP CYS CYS ILE ARG GLU VAL LYS SEQRES 5 B 146 GLU GLN ILE GLY PHE ASP LEU THR ASP TYR ILE ASP ASP SEQRES 6 B 146 ASN GLN PHE ILE GLU ARG ASN ILE GLN GLY LYS ASN TYR SEQRES 7 B 146 LYS ILE PHE LEU ILE SER GLY VAL SER GLU VAL PHE ASN SEQRES 8 B 146 PHE LYS PRO GLN VAL ARG ASN GLU ILE ASP LYS ILE GLU SEQRES 9 B 146 TRP PHE ASP PHE LYS LYS ILE SER LYS THR MET TYR LYS SEQRES 10 B 146 SER ASN ILE LYS TYR TYR LEU ILE ASN SER MET MET ARG SEQRES 11 B 146 PRO LEU SER MET TRP LEU ARG HIS GLN ARG GLN ILE LYS SEQRES 12 B 146 ASN GLU ASP SEQRES 1 C 146 LYS LYS SER ILE PRO VAL ARG GLY ALA ALA ILE PHE ASN SEQRES 2 C 146 GLU ASN LEU SER LYS ILE LEU LEU VAL GLN GLY THR GLU SEQRES 3 C 146 SER ASP SER TRP SER PHE PRO ARG GLY LYS ILE SER LYS SEQRES 4 C 146 ASP GLU ASN ASP ILE ASP CYS CYS ILE ARG GLU VAL LYS SEQRES 5 C 146 GLU GLN ILE GLY PHE ASP LEU THR ASP TYR ILE ASP ASP SEQRES 6 C 146 ASN GLN PHE ILE GLU ARG ASN ILE GLN GLY LYS ASN TYR SEQRES 7 C 146 LYS ILE PHE LEU ILE SER GLY VAL SER GLU VAL PHE ASN SEQRES 8 C 146 PHE LYS PRO GLN VAL ARG ASN GLU ILE ASP LYS ILE GLU SEQRES 9 C 146 TRP PHE ASP PHE LYS LYS ILE SER LYS THR MET TYR LYS SEQRES 10 C 146 SER ASN ILE LYS TYR TYR LEU ILE ASN SER MET MET ARG SEQRES 11 C 146 PRO LEU SER MET TRP LEU ARG HIS GLN ARG GLN ILE LYS SEQRES 12 C 146 ASN GLU ASP HET MG A 301 1 HET MG B 301 1 HET MG C 301 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *356(H2 O) HELIX 1 1 ASN A 141 GLY A 155 1 15 HELIX 2 2 PHE A 207 MET A 214 1 8 HELIX 3 3 TYR A 215 SER A 217 5 3 HELIX 4 4 LEU A 223 SER A 226 5 4 HELIX 5 5 MET A 227 GLN A 238 1 12 HELIX 6 6 ASN B 141 GLY B 155 1 15 HELIX 7 7 PHE B 207 MET B 214 1 8 HELIX 8 8 LEU B 223 SER B 226 5 4 HELIX 9 9 MET B 227 ILE B 241 1 15 HELIX 10 10 LYS B 242 ASP B 245 5 4 HELIX 11 11 ASN C 141 GLY C 155 1 15 HELIX 12 12 PHE C 207 LYS C 212 1 6 HELIX 13 13 LEU C 223 SER C 226 5 4 HELIX 14 14 MET C 227 ILE C 241 1 15 HELIX 15 15 LYS C 242 ASP C 245 5 4 SHEET 1 A 4 ARG A 133 LYS A 135 0 SHEET 2 A 4 VAL A 105 ASN A 112 -1 N ARG A 106 O GLY A 134 SHEET 3 A 4 LYS A 175 VAL A 185 1 O PHE A 180 N ALA A 109 SHEET 4 A 4 PHE A 167 ILE A 172 -1 N ARG A 170 O TYR A 177 SHEET 1 B 3 TRP A 129 SER A 130 0 SHEET 2 B 3 LYS A 117 GLY A 123 -1 N VAL A 121 O SER A 130 SHEET 3 B 3 ILE A 199 ASP A 206 -1 O ASP A 200 N GLN A 122 SHEET 1 C 5 TRP B 129 SER B 130 0 SHEET 2 C 5 LYS B 117 GLY B 123 -1 N VAL B 121 O SER B 130 SHEET 3 C 5 VAL B 105 ASN B 112 -1 N ILE B 110 O LEU B 119 SHEET 4 C 5 LYS B 175 VAL B 185 1 O PHE B 180 N ALA B 109 SHEET 5 C 5 PHE B 167 ILE B 172 -1 N ILE B 168 O ILE B 179 SHEET 1 D 4 ARG B 133 LYS B 135 0 SHEET 2 D 4 VAL B 105 ASN B 112 -1 N ARG B 106 O GLY B 134 SHEET 3 D 4 LYS B 117 GLY B 123 -1 O LEU B 119 N ILE B 110 SHEET 4 D 4 ILE B 199 ASP B 206 -1 O PHE B 205 N ILE B 118 SHEET 1 E 5 TRP C 129 SER C 130 0 SHEET 2 E 5 LYS C 117 GLY C 123 -1 N VAL C 121 O SER C 130 SHEET 3 E 5 VAL C 105 PHE C 111 -1 N ILE C 110 O LEU C 119 SHEET 4 E 5 LYS C 175 ILE C 182 1 O ASN C 176 N VAL C 105 SHEET 5 E 5 PHE C 167 ILE C 172 -1 N ARG C 170 O TYR C 177 SHEET 1 F 4 ARG C 133 LYS C 135 0 SHEET 2 F 4 VAL C 105 PHE C 111 -1 N ARG C 106 O GLY C 134 SHEET 3 F 4 LYS C 117 GLY C 123 -1 O LEU C 119 N ILE C 110 SHEET 4 F 4 ILE C 199 ASP C 206 -1 O PHE C 205 N ILE C 118 LINK OE1 GLU A 149 MG MG A 301 1555 1555 2.02 LINK MG MG A 301 O HOH A 401 1555 1555 2.10 LINK MG MG A 301 O HOH A 406 1555 1555 2.06 LINK MG MG A 301 O HOH A 408 1555 1555 2.10 LINK MG MG A 301 O HOH A 412 1555 1555 2.09 LINK MG MG A 301 O HOH A 513 1555 1555 2.06 LINK OE1 GLU B 149 MG MG B 301 1555 1555 2.06 LINK MG MG B 301 O HOH B 403 1555 1555 2.13 LINK MG MG B 301 O HOH B 406 1555 1555 2.07 LINK MG MG B 301 O HOH C 402 1555 1555 2.09 LINK MG MG B 301 O HOH C 404 1555 1555 2.00 LINK MG MG B 301 O HOH C 532 1555 1555 1.98 LINK OE1 GLU C 149 MG MG C 301 1555 1555 2.13 LINK MG MG C 301 O HOH C 416 1555 1555 2.09 LINK MG MG C 301 O HOH C 419 1555 1555 2.01 LINK MG MG C 301 O HOH C 434 1555 1555 2.06 LINK MG MG C 301 O HOH C 486 1555 1555 2.09 LINK MG MG C 301 O HOH C 533 1555 1555 2.06 CISPEP 1 TYR C 215 LYS C 216 0 -17.02 SITE 1 AC1 6 GLU A 149 HOH A 401 HOH A 406 HOH A 408 SITE 2 AC1 6 HOH A 412 HOH A 513 SITE 1 AC2 6 GLU B 149 HOH B 403 HOH B 406 HOH C 402 SITE 2 AC2 6 HOH C 404 HOH C 532 SITE 1 AC3 6 GLU C 149 HOH C 416 HOH C 419 HOH C 434 SITE 2 AC3 6 HOH C 486 HOH C 533 CRYST1 140.789 49.270 84.022 90.00 91.37 90.00 C 1 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 0.007103 0.000000 0.000170 0.00000 SCALE2 0.000000 0.020296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011905 0.00000