HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DO8 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2 MM MG2+ AND 200 MM K+ FOR 80 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 14 CHAIN: b; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; 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; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 13-MAR-24 6DO8 1 LINK REVDAT 1 15-AUG-18 6DO8 0 JRNL AUTH N.L.SAMARA,W.YANG JRNL TITL CATION TRAFFICKING PROPELS RNA HYDROLYSIS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 715 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 30076410 JRNL DOI 10.1038/S41594-018-0099-4 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 34741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1735 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 19.8470 - 3.2337 0.99 2920 169 0.1256 0.1438 REMARK 3 2 3.2337 - 2.5684 0.99 2836 163 0.1442 0.1516 REMARK 3 3 2.5684 - 2.2443 0.98 2841 121 0.1394 0.1439 REMARK 3 4 2.2443 - 2.0393 0.98 2799 155 0.1350 0.1816 REMARK 3 5 2.0393 - 1.8932 0.98 2792 137 0.1435 0.1608 REMARK 3 6 1.8932 - 1.7817 0.97 2760 145 0.1535 0.1679 REMARK 3 7 1.7817 - 1.6925 0.97 2785 143 0.1619 0.1936 REMARK 3 8 1.6925 - 1.6189 0.97 2708 162 0.1839 0.2122 REMARK 3 9 1.6189 - 1.5566 0.96 2712 135 0.1890 0.2261 REMARK 3 10 1.5566 - 1.5029 0.96 2710 147 0.2260 0.2469 REMARK 3 11 1.5029 - 1.4559 0.95 2667 146 0.2703 0.2903 REMARK 3 12 1.4559 - 1.4143 0.85 2476 112 0.3196 0.3518 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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 : 0.008 1468 REMARK 3 ANGLE : 1.031 2027 REMARK 3 CHIRALITY : 0.070 220 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 23.135 577 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 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.875 -3.977 18.913 REMARK 3 T TENSOR REMARK 3 T11: 0.1992 T22: 0.4494 REMARK 3 T33: 0.3081 T12: 0.1000 REMARK 3 T13: 0.0682 T23: 0.0416 REMARK 3 L TENSOR REMARK 3 L11: 2.2454 L22: 2.8983 REMARK 3 L33: 6.2886 L12: -0.5531 REMARK 3 L13: -0.5333 L23: -1.3803 REMARK 3 S TENSOR REMARK 3 S11: 0.1057 S12: 0.6248 S13: -0.0842 REMARK 3 S21: -0.4513 S22: -0.5190 S23: -0.8536 REMARK 3 S31: 0.0931 S32: 1.2111 S33: 0.3700 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.607 -6.353 16.238 REMARK 3 T TENSOR REMARK 3 T11: 0.1875 T22: 0.1472 REMARK 3 T33: 0.1839 T12: -0.0050 REMARK 3 T13: -0.0173 T23: 0.0209 REMARK 3 L TENSOR REMARK 3 L11: 2.1111 L22: 1.1546 REMARK 3 L33: 2.5956 L12: 0.4020 REMARK 3 L13: 1.6990 L23: 1.4737 REMARK 3 S TENSOR REMARK 3 S11: 0.4506 S12: -0.1355 S13: -0.3465 REMARK 3 S21: -0.1589 S22: -0.2662 S23: 0.0503 REMARK 3 S31: 0.4901 S32: -0.2418 S33: -0.1550 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 76:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.063 -6.625 16.723 REMARK 3 T TENSOR REMARK 3 T11: 0.1803 T22: 0.1136 REMARK 3 T33: 0.1753 T12: -0.0001 REMARK 3 T13: -0.0071 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 7.5814 L22: 0.7407 REMARK 3 L33: 6.8105 L12: -0.4304 REMARK 3 L13: 5.7190 L23: -0.7299 REMARK 3 S TENSOR REMARK 3 S11: 0.3864 S12: 0.1430 S13: -0.4680 REMARK 3 S21: -0.1658 S22: -0.2171 S23: 0.0681 REMARK 3 S31: 0.3651 S32: -0.0367 S33: -0.2090 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.126 -11.490 24.008 REMARK 3 T TENSOR REMARK 3 T11: 0.2308 T22: 0.1456 REMARK 3 T33: 0.3173 T12: 0.0544 REMARK 3 T13: 0.0035 T23: 0.0399 REMARK 3 L TENSOR REMARK 3 L11: 4.0420 L22: 6.0804 REMARK 3 L33: 7.7345 L12: -2.6081 REMARK 3 L13: -4.1235 L23: 0.7006 REMARK 3 S TENSOR REMARK 3 S11: -0.1452 S12: -0.4792 S13: -1.1289 REMARK 3 S21: -0.0489 S22: 0.1093 S23: -0.4417 REMARK 3 S31: 0.9159 S32: 0.3981 S33: 0.0533 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.464 -5.100 18.627 REMARK 3 T TENSOR REMARK 3 T11: 0.1614 T22: 0.2495 REMARK 3 T33: 0.1707 T12: -0.0241 REMARK 3 T13: -0.0107 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 5.6310 L22: 3.4280 REMARK 3 L33: 9.1295 L12: -1.6588 REMARK 3 L13: 1.8521 L23: -5.4690 REMARK 3 S TENSOR REMARK 3 S11: 0.1409 S12: -0.3872 S13: -0.4590 REMARK 3 S21: -0.0313 S22: 0.2719 S23: 0.5291 REMARK 3 S31: 0.1501 S32: -1.1081 S33: -0.3479 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.117 0.634 23.949 REMARK 3 T TENSOR REMARK 3 T11: 0.1004 T22: 0.0895 REMARK 3 T33: 0.1206 T12: 0.0095 REMARK 3 T13: 0.0344 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 4.5500 L22: 1.6819 REMARK 3 L33: 5.2895 L12: -0.6100 REMARK 3 L13: 3.3720 L23: 0.5807 REMARK 3 S TENSOR REMARK 3 S11: 0.0302 S12: -0.2413 S13: -0.0293 REMARK 3 S21: -0.0505 S22: -0.0804 S23: 0.0374 REMARK 3 S31: -0.0760 S32: -0.2765 S33: 0.0218 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 123:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.949 -0.856 25.385 REMARK 3 T TENSOR REMARK 3 T11: 0.1022 T22: 0.1000 REMARK 3 T33: 0.1347 T12: -0.0017 REMARK 3 T13: 0.0217 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 3.6945 L22: 1.4827 REMARK 3 L33: 6.2559 L12: -0.7559 REMARK 3 L13: 2.8175 L23: 0.1982 REMARK 3 S TENSOR REMARK 3 S11: 0.0755 S12: -0.0843 S13: -0.0260 REMARK 3 S21: -0.0257 S22: -0.0400 S23: -0.0632 REMARK 3 S31: 0.2100 S32: 0.1851 S33: -0.0135 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.939 8.787 16.159 REMARK 3 T TENSOR REMARK 3 T11: 0.2445 T22: 0.0829 REMARK 3 T33: 0.1730 T12: -0.0024 REMARK 3 T13: 0.0237 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 4.7147 L22: 6.9277 REMARK 3 L33: 7.0209 L12: -3.6787 REMARK 3 L13: -1.7621 L23: -0.6804 REMARK 3 S TENSOR REMARK 3 S11: 0.1538 S12: 0.1355 S13: 0.3817 REMARK 3 S21: -0.1780 S22: -0.1606 S23: -0.2964 REMARK 3 S31: -0.8326 S32: 0.1897 S33: -0.0119 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 142:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.564 7.877 16.402 REMARK 3 T TENSOR REMARK 3 T11: 0.3472 T22: 0.3708 REMARK 3 T33: 0.2189 T12: 0.2471 REMARK 3 T13: -0.0193 T23: -0.1028 REMARK 3 L TENSOR REMARK 3 L11: 7.0649 L22: 3.8472 REMARK 3 L33: 2.4312 L12: 2.1605 REMARK 3 L13: 2.3345 L23: 0.1103 REMARK 3 S TENSOR REMARK 3 S11: 0.3102 S12: 0.0666 S13: 0.5135 REMARK 3 S21: -0.1256 S22: -0.4347 S23: 0.4636 REMARK 3 S31: -0.4764 S32: -0.6793 S33: 0.1471 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.367 5.707 24.863 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.2242 REMARK 3 T33: 0.1528 T12: 0.0706 REMARK 3 T13: 0.0236 T23: -0.0458 REMARK 3 L TENSOR REMARK 3 L11: 7.9805 L22: 1.7876 REMARK 3 L33: 7.1265 L12: 1.2545 REMARK 3 L13: 5.9197 L23: 2.1386 REMARK 3 S TENSOR REMARK 3 S11: 0.1744 S12: -0.2441 S13: 0.0312 REMARK 3 S21: -0.0037 S22: -0.3052 S23: 0.1882 REMARK 3 S31: -0.1529 S32: -0.7136 S33: 0.1593 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.966 8.490 30.399 REMARK 3 T TENSOR REMARK 3 T11: 0.1657 T22: 0.1430 REMARK 3 T33: 0.1668 T12: -0.0044 REMARK 3 T13: -0.0027 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 8.1760 L22: 5.3867 REMARK 3 L33: 7.8032 L12: -4.8007 REMARK 3 L13: -6.6477 L23: 3.8037 REMARK 3 S TENSOR REMARK 3 S11: 0.1387 S12: -0.5453 S13: 0.6848 REMARK 3 S21: -0.0588 S22: 0.2213 S23: -0.3857 REMARK 3 S31: -0.3437 S32: 0.3493 S33: -0.2631 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.611 -0.692 12.319 REMARK 3 T TENSOR REMARK 3 T11: 0.2472 T22: 0.3200 REMARK 3 T33: 0.1994 T12: 0.0740 REMARK 3 T13: 0.1006 T23: 0.0341 REMARK 3 L TENSOR REMARK 3 L11: 2.8610 L22: 5.5893 REMARK 3 L33: 6.3850 L12: 0.0985 REMARK 3 L13: -0.5871 L23: 4.6086 REMARK 3 S TENSOR REMARK 3 S11: 0.1401 S12: 0.5658 S13: -0.0404 REMARK 3 S21: -0.7281 S22: -0.0083 S23: -0.5995 REMARK 3 S31: -0.1066 S32: 0.7443 S33: -0.1932 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.770 -9.677 12.527 REMARK 3 T TENSOR REMARK 3 T11: 0.4032 T22: 0.2411 REMARK 3 T33: 0.1968 T12: 0.0168 REMARK 3 T13: -0.0071 T23: -0.0825 REMARK 3 L TENSOR REMARK 3 L11: 5.6647 L22: 6.3227 REMARK 3 L33: 8.5867 L12: -0.1098 REMARK 3 L13: -6.1582 L23: 0.0798 REMARK 3 S TENSOR REMARK 3 S11: -0.2522 S12: 0.9361 S13: -0.7021 REMARK 3 S21: -0.7693 S22: 0.0374 S23: 0.1937 REMARK 3 S31: 0.8808 S32: -0.3423 S33: 0.1541 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) OR ( CHAIN B AND RESID 5:6 REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.753 1.230 4.530 REMARK 3 T TENSOR REMARK 3 T11: 0.3018 T22: 0.2175 REMARK 3 T33: 0.1480 T12: 0.0850 REMARK 3 T13: 0.0364 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.2302 L22: 3.4764 REMARK 3 L33: 5.8746 L12: -1.3275 REMARK 3 L13: 2.2482 L23: -0.8988 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: 0.4990 S13: -0.0224 REMARK 3 S21: -0.5606 S22: -0.2445 S23: -0.1969 REMARK 3 S31: -0.0511 S32: 0.3207 S33: 0.2576 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.355 3.538 3.195 REMARK 3 T TENSOR REMARK 3 T11: 0.4117 T22: 0.2104 REMARK 3 T33: 0.1619 T12: 0.1046 REMARK 3 T13: -0.0255 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.5918 L22: 2.1999 REMARK 3 L33: 6.2490 L12: -1.6109 REMARK 3 L13: -2.6120 L23: 0.2709 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.4021 S13: -0.1615 REMARK 3 S21: -0.8611 S22: -0.3712 S23: 0.1466 REMARK 3 S31: -0.3547 S32: -0.2727 S33: 0.3090 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 6DO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34747 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 19.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM KI, REMARK 280 AND 25 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.64200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.88900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.64200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.88900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 LYS A 196 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 A B 1 O2' REMARK 470 G b 6 O2' 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' -0.053 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 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES 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 452 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 7.51 ANGSTROMS 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 102.8 REMARK 620 3 HOH A 308 O 174.2 72.4 REMARK 620 4 HOH A 318 O 90.5 95.7 87.0 REMARK 620 5 HOH A 338 O 90.4 91.8 92.9 172.1 REMARK 620 6 C b 5 OP1 101.0 155.5 84.2 89.6 82.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 100.6 REMARK 620 3 ASP A 132 OD1 138.8 94.9 REMARK 620 4 ASP A 132 OD2 115.6 141.2 48.6 REMARK 620 5 U B 4 O3' 137.6 79.9 82.5 82.1 REMARK 620 6 C b 5 OP1 85.7 107.6 125.3 89.2 54.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ARG A 195 O 145.4 REMARK 620 3 HOH A 308 O 51.5 109.9 REMARK 620 4 HOH A 317 O 67.5 77.9 61.2 REMARK 620 5 HOH A 318 O 56.1 147.8 61.2 116.0 REMARK 620 6 G b 6 OP2 103.9 94.2 71.5 125.0 53.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 108 O REMARK 620 2 DT C 4 O4 157.6 REMARK 620 3 DG C 5 O6 86.1 76.4 REMARK 620 4 HOH C 207 O 104.2 87.6 82.9 REMARK 620 N 1 2 3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DMV RELATED DB: PDB REMARK 900 6DMV CONTAINS THE SAME COMPLEX SOAKED IN DIFFERENT CONDITIONS REMARK 900 RELATED ID: 6DMN RELATED DB: PDB REMARK 900 6DMN CONTAINS THE SAME COMPLEX SOAKED IN DIFFERENT CONDITIONS DBREF 6DO8 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DO8 B 1 4 PDB 6DO8 6DO8 1 4 DBREF 6DO8 b 5 6 PDB 6DO8 6DO8 5 6 DBREF 6DO8 C 1 6 PDB 6DO8 6DO8 1 6 SEQADV 6DO8 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DO8 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DO8 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DO8 MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASP SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET GOL A 211 6 HET EDO A 212 4 HET EDO A 213 4 HET GOL A 214 6 HET K C 101 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 2(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 5(C3 H8 O3) FORMUL 16 EDO 2(C2 H6 O2) FORMUL 20 HOH *186(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 THR A 155 ASN A 170 1 16 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 5 VAL A 93 GLY A 103 0 SHEET 2 AA1 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 AA1 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA1 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA1 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' U B 4 P C b 5 1555 1555 1.60 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.94 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.04 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.39 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.34 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.87 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.96 LINK OD1 ASP A 192 K K A 203 1555 1555 3.11 LINK O ARG A 195 K K A 203 1555 1555 3.02 LINK MG MG A 201 O HOH A 308 1555 1555 2.33 LINK MG MG A 201 O HOH A 318 1555 1555 2.01 LINK MG MG A 201 O HOH A 338 1555 1555 2.16 LINK MG MG A 201 OP1 C b 5 1555 1555 2.11 LINK MG MG A 202 O3' U B 4 1555 1555 2.77 LINK MG MG A 202 OP1 C b 5 1555 1555 2.56 LINK K K A 203 O HOH A 308 1555 1555 2.70 LINK K K A 203 O HOH A 317 1555 1555 2.74 LINK K K A 203 O HOH A 318 1555 1555 3.14 LINK K K A 203 OP2 G b 6 1555 1555 2.99 LINK O HOH B 108 K A K C 101 1555 1555 3.31 LINK O4 DT C 4 K A K C 101 1555 1555 3.13 LINK O6 DG C 5 K A K C 101 1555 1555 2.64 LINK K A K C 101 O HOH C 207 1555 1555 3.14 CISPEP 1 ASN A 77 PRO A 78 0 1.62 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 308 HOH A 318 SITE 2 AC1 6 HOH A 338 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 6 ASP A 192 GLY A 194 ARG A 195 HOH A 308 SITE 2 AC3 6 HOH A 317 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 450 HOH A 453 SITE 1 AC6 2 HIS A 172 HOH A 434 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 369 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 8 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC8 8 GLU A 167 ASN A 170 GOL A 211 HOH A 305 SITE 1 AC9 6 GLU A 66 LEU A 94 SER A 125 LYS A 127 SITE 2 AC9 6 HOH A 304 HOH A 339 SITE 1 AD1 5 HIS A 115 ASN A 170 GOL A 209 HOH A 307 SITE 2 AD1 5 HOH A 353 SITE 1 AD2 4 LYS A 143 THR A 173 TYR A 174 HOH A 367 SITE 1 AD3 4 LYS A 89 GLU A 153 ALA A 156 HOH A 435 SITE 1 AD4 5 THR A 148 HOH A 385 DT C 4 DG C 5 SITE 2 AD4 5 HOH C 201 SITE 1 AD5 3 DT C 4 DG C 5 HOH C 211 CRYST1 81.284 37.778 62.072 90.00 96.22 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012303 0.000000 0.001341 0.00000 SCALE2 0.000000 0.026470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016206 0.00000