HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP7 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 500 MM MN2+ AND 200 MM K+ FOR 40 TITLE 3 S AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 13 CHAIN: b; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 6 GENE: RNHA, BH0863; 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: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 23 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-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DP7 1 LINK REVDAT 1 15-AUG-18 6DP7 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. 1.38 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 37887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1908 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 17.9841 - 3.3212 0.94 2539 144 0.1397 0.1817 REMARK 3 2 3.3212 - 2.6388 1.00 2652 142 0.1571 0.1636 REMARK 3 3 2.6388 - 2.3060 1.00 2625 154 0.1585 0.1643 REMARK 3 4 2.3060 - 2.0955 1.00 2633 135 0.1764 0.1855 REMARK 3 5 2.0955 - 1.9455 1.00 2612 142 0.1762 0.1970 REMARK 3 6 1.9455 - 1.8309 0.98 2570 125 0.2231 0.2626 REMARK 3 7 1.8309 - 1.7393 1.00 2601 141 0.1772 0.2216 REMARK 3 8 1.7393 - 1.6636 1.00 2626 145 0.1778 0.2021 REMARK 3 9 1.6636 - 1.5996 1.00 2630 118 0.1794 0.2135 REMARK 3 10 1.5996 - 1.5445 1.00 2601 124 0.1942 0.2029 REMARK 3 11 1.5445 - 1.4962 0.98 2559 148 0.2367 0.2252 REMARK 3 12 1.4962 - 1.4535 0.99 2571 121 0.2385 0.2941 REMARK 3 13 1.4535 - 1.4152 0.99 2599 141 0.2481 0.2735 REMARK 3 14 1.4152 - 1.3807 0.83 2161 128 0.2465 0.3005 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.36 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 1426 REMARK 3 ANGLE : 0.946 1969 REMARK 3 CHIRALITY : 0.073 217 REMARK 3 PLANARITY : 0.006 207 REMARK 3 DIHEDRAL : 23.788 549 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 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.675 -4.273 18.623 REMARK 3 T TENSOR REMARK 3 T11: 0.2379 T22: 0.5174 REMARK 3 T33: 0.3106 T12: 0.0514 REMARK 3 T13: 0.0685 T23: -0.0505 REMARK 3 L TENSOR REMARK 3 L11: 3.8197 L22: 8.7650 REMARK 3 L33: 2.7436 L12: -0.0377 REMARK 3 L13: 1.5754 L23: -2.8629 REMARK 3 S TENSOR REMARK 3 S11: 0.0881 S12: 0.3356 S13: 0.1769 REMARK 3 S21: -0.8294 S22: 0.0056 S23: -1.4633 REMARK 3 S31: 0.0032 S32: 1.9849 S33: 0.2672 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.716 -6.121 16.521 REMARK 3 T TENSOR REMARK 3 T11: 0.2010 T22: 0.1888 REMARK 3 T33: 0.1411 T12: 0.0018 REMARK 3 T13: 0.0109 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 4.8076 L22: 2.1723 REMARK 3 L33: 4.9354 L12: -2.2546 REMARK 3 L13: 4.8138 L23: -2.0684 REMARK 3 S TENSOR REMARK 3 S11: 0.3283 S12: 0.1314 S13: -0.4796 REMARK 3 S21: -0.2138 S22: -0.0409 S23: 0.1212 REMARK 3 S31: 0.3599 S32: -0.1526 S33: -0.3352 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.981 -11.665 23.753 REMARK 3 T TENSOR REMARK 3 T11: 0.2438 T22: 0.2706 REMARK 3 T33: 0.3283 T12: 0.0688 REMARK 3 T13: 0.0281 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 2.0024 L22: 2.0187 REMARK 3 L33: 2.5550 L12: -0.7884 REMARK 3 L13: -0.2177 L23: 2.0334 REMARK 3 S TENSOR REMARK 3 S11: 0.1012 S12: -0.2136 S13: -1.7450 REMARK 3 S21: 0.1007 S22: -0.1155 S23: -0.4178 REMARK 3 S31: 0.5899 S32: 0.4032 S33: 0.1150 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.095 -0.958 22.306 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.1449 REMARK 3 T33: 0.0830 T12: 0.0063 REMARK 3 T13: 0.0388 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 5.4480 L22: 2.2244 REMARK 3 L33: 4.9627 L12: 0.0196 REMARK 3 L13: 3.4091 L23: 0.3663 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: -0.3392 S13: -0.1429 REMARK 3 S21: -0.0264 S22: -0.0978 S23: 0.0897 REMARK 3 S31: 0.0926 S32: -0.5848 S33: 0.0326 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 123:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.146 -1.102 25.288 REMARK 3 T TENSOR REMARK 3 T11: 0.1154 T22: 0.1698 REMARK 3 T33: 0.1077 T12: -0.0017 REMARK 3 T13: 0.0330 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 4.3695 L22: 3.1097 REMARK 3 L33: 4.3659 L12: -1.0573 REMARK 3 L13: 2.1932 L23: 0.9017 REMARK 3 S TENSOR REMARK 3 S11: 0.0907 S12: -0.3300 S13: -0.0428 REMARK 3 S21: 0.1235 S22: -0.0145 S23: -0.2231 REMARK 3 S31: 0.4138 S32: -0.0830 S33: -0.0452 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.959 9.471 16.624 REMARK 3 T TENSOR REMARK 3 T11: 0.2562 T22: 0.1367 REMARK 3 T33: 0.1477 T12: -0.0052 REMARK 3 T13: 0.0540 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 8.9191 L22: 7.6057 REMARK 3 L33: 2.3234 L12: -6.3950 REMARK 3 L13: -2.2599 L23: 3.6715 REMARK 3 S TENSOR REMARK 3 S11: 0.1613 S12: 0.2310 S13: 0.7337 REMARK 3 S21: -0.3288 S22: -0.0519 S23: -0.6413 REMARK 3 S31: -0.7036 S32: 0.3228 S33: -0.1565 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.596 7.762 16.126 REMARK 3 T TENSOR REMARK 3 T11: 0.2239 T22: 0.3078 REMARK 3 T33: 0.2035 T12: 0.1621 REMARK 3 T13: -0.0002 T23: -0.0981 REMARK 3 L TENSOR REMARK 3 L11: 5.6295 L22: 7.8424 REMARK 3 L33: 8.3431 L12: -0.9059 REMARK 3 L13: 4.0658 L23: 0.9704 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: 0.0737 S13: 0.4592 REMARK 3 S21: -0.3623 S22: -0.3071 S23: 0.7589 REMARK 3 S31: -0.2835 S32: -0.6341 S33: 0.1865 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:171 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.219 6.516 25.533 REMARK 3 T TENSOR REMARK 3 T11: 0.1862 T22: 0.2415 REMARK 3 T33: 0.1488 T12: 0.0648 REMARK 3 T13: -0.0021 T23: -0.0460 REMARK 3 L TENSOR REMARK 3 L11: 2.7897 L22: 4.3395 REMARK 3 L33: 7.4550 L12: 3.1939 REMARK 3 L13: 1.9457 L23: 3.5303 REMARK 3 S TENSOR REMARK 3 S11: 0.0372 S12: -0.4568 S13: 0.3056 REMARK 3 S21: 0.0068 S22: -0.3389 S23: 0.1762 REMARK 3 S31: -0.2520 S32: -0.8371 S33: 0.3278 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 172:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.474 7.324 29.944 REMARK 3 T TENSOR REMARK 3 T11: 0.2259 T22: 0.2566 REMARK 3 T33: 0.2402 T12: -0.0213 REMARK 3 T13: -0.0093 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 3.7457 L22: 5.5613 REMARK 3 L33: 4.5113 L12: 0.2018 REMARK 3 L13: 0.5531 L23: 4.9595 REMARK 3 S TENSOR REMARK 3 S11: 0.0761 S12: -0.8659 S13: 1.0407 REMARK 3 S21: 0.2377 S22: 0.3537 S23: -0.6380 REMARK 3 S31: -0.1263 S32: 0.8671 S33: -0.3400 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.447 -0.933 12.140 REMARK 3 T TENSOR REMARK 3 T11: 0.2235 T22: 0.3389 REMARK 3 T33: 0.1718 T12: 0.0478 REMARK 3 T13: 0.0845 T23: 0.0225 REMARK 3 L TENSOR REMARK 3 L11: 0.4038 L22: 4.1396 REMARK 3 L33: 8.7824 L12: -0.9826 REMARK 3 L13: -1.1911 L23: 5.9334 REMARK 3 S TENSOR REMARK 3 S11: 0.2313 S12: 0.5969 S13: 0.0550 REMARK 3 S21: -0.5343 S22: -0.1220 S23: -0.4807 REMARK 3 S31: -0.3113 S32: 0.3665 S33: -0.1666 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.529 -9.757 12.266 REMARK 3 T TENSOR REMARK 3 T11: 0.2541 T22: 0.2444 REMARK 3 T33: 0.1645 T12: 0.0715 REMARK 3 T13: -0.0121 T23: -0.0558 REMARK 3 L TENSOR REMARK 3 L11: 5.2247 L22: 7.1588 REMARK 3 L33: 4.6347 L12: 1.0068 REMARK 3 L13: -4.3952 L23: 1.7051 REMARK 3 S TENSOR REMARK 3 S11: 0.1945 S12: 0.6405 S13: -0.7039 REMARK 3 S21: -0.2731 S22: -0.2194 S23: 0.0833 REMARK 3 S31: 0.3012 S32: 0.0563 S33: 0.0072 REMARK 3 TLS GROUP : 12 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): 23.906 1.269 4.468 REMARK 3 T TENSOR REMARK 3 T11: 0.3017 T22: 0.2431 REMARK 3 T33: 0.1557 T12: 0.0835 REMARK 3 T13: 0.0803 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 1.5058 L22: 5.9214 REMARK 3 L33: 5.4874 L12: -1.8710 REMARK 3 L13: 2.6525 L23: -3.1615 REMARK 3 S TENSOR REMARK 3 S11: 0.2808 S12: 0.0952 S13: 0.0397 REMARK 3 S21: -0.5396 S22: -0.6696 S23: -0.4994 REMARK 3 S31: -0.0114 S32: 0.4963 S33: 0.3374 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.451 3.798 3.062 REMARK 3 T TENSOR REMARK 3 T11: 0.4166 T22: 0.2269 REMARK 3 T33: 0.1234 T12: 0.0940 REMARK 3 T13: -0.0353 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 1.2053 L22: 4.0600 REMARK 3 L33: 7.6242 L12: -1.7941 REMARK 3 L13: -2.8661 L23: 3.2272 REMARK 3 S TENSOR REMARK 3 S11: 0.0815 S12: 0.1634 S13: 0.0630 REMARK 3 S21: -1.1326 S22: -0.5584 S23: 0.3238 REMARK 3 S31: -0.8268 S32: -0.5920 S33: 0.3913 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 6DP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-17 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 : 23-BM-B 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 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38088 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 17.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 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: PHENIX REMARK 200 STARTING MODEL: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.90 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 41.00650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.77850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.00650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.77850 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: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 400 REMARK 400 COMPOUND REMARK 400 NOTE THAT CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) AT THE POSITION REMARK 400 4-5, WHERE THE CLEAVAGE DOES OCCUR 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: 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 B 103 O HOH B 108 2.15 REMARK 500 O HOH b 203 O HOH b 207 2.18 REMARK 500 OH TYR A 174 O HOH A 302 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH b 210 O HOH C 216 4545 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C b 5 P C b 5 OP3 -0.116 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 431 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH b 209 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH b 210 DISTANCE = 6.86 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 108.7 REMARK 620 3 HOH A 341 O 89.8 88.8 REMARK 620 4 C b 5 OP3 154.6 96.4 94.5 REMARK 620 5 C b 5 OP1 95.2 154.7 83.0 60.7 REMARK 620 6 HOH b 201 O 88.5 85.5 173.1 89.9 103.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 96.9 REMARK 620 3 ASP A 132 OD1 128.3 95.8 REMARK 620 4 ASP A 132 OD2 101.6 149.5 53.8 REMARK 620 5 C b 5 OP1 95.5 113.5 124.0 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 163 OD1 REMARK 620 2 GLU A 166 OE1 97.3 REMARK 620 3 HOH A 332 O 98.0 88.4 REMARK 620 4 HOH A 355 O 171.1 88.6 88.8 REMARK 620 5 HOH A 394 O 87.0 92.8 174.6 86.0 REMARK 620 6 HOH A 396 O 97.3 165.1 92.6 76.5 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 204 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 HOH A 338 O 69.8 REMARK 620 3 HOH A 341 O 55.7 58.9 REMARK 620 4 HOH B 103 O 125.1 114.5 173.2 REMARK 620 5 C b 5 OP2 113.8 127.2 79.6 104.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN b 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 301 O REMARK 620 2 C b 5 OP3 172.4 REMARK 620 3 G b 6 OP2 91.0 82.2 REMARK 620 4 HOH b 204 O 109.7 77.9 146.7 REMARK 620 5 HOH b 205 O 82.0 98.3 66.9 89.8 REMARK 620 6 HOH b 208 O 64.4 118.2 133.1 80.1 138.6 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 MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 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 EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN b 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 DBREF 6DP7 A 61 195 UNP Q9KEI9 RNH1_BACHD 61 195 DBREF 6DP7 B 1 4 PDB 6DP7 6DP7 1 4 DBREF 6DP7 b 5 6 PDB 6DP7 6DP7 5 6 DBREF 6DP7 C 1 6 PDB 6DP7 6DP7 1 6 SEQRES 1 A 135 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 135 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 135 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 135 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 135 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 135 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 135 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 135 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 135 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 135 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 135 ALA ASP TYR GLY ARG 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 MN A 201 1 HET MN A 202 1 HET MN A 203 1 HET K A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET EDO A 208 4 HET MN b 101 1 HET EDO C 101 4 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 4(MN 2+) FORMUL 8 K K 1+ FORMUL 9 IOD 3(I 1-) FORMUL 12 EDO 2(C2 H6 O2) FORMUL 15 HOH *169(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 HIS A 172 1 18 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK OD2 ASP A 71 MN MN A 201 1555 1555 2.07 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.08 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.08 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.13 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.62 LINK OD1 ASP A 163 MN MN A 203 1555 1555 2.40 LINK OE1 GLU A 166 MN MN A 203 1555 1555 2.20 LINK OE2 GLU A 188 K K A 204 1555 1555 2.86 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.06 LINK MN MN A 201 O HOH A 341 1555 1555 2.18 LINK MN MN A 201 OP3A C b 5 1555 1555 2.21 LINK MN MN A 201 OP1A C b 5 1555 1555 2.50 LINK MN MN A 201 O HOH b 201 1555 1555 2.18 LINK MN MN A 202 OP1A C b 5 1555 1555 2.06 LINK MN MN A 203 O HOH A 332 1555 1555 2.18 LINK MN MN A 203 O HOH A 355 1555 1555 1.83 LINK MN MN A 203 O HOH A 394 1555 1555 2.10 LINK MN MN A 203 O HOH A 396 1555 1555 2.10 LINK K K A 204 O HOH A 338 1555 1555 3.32 LINK K K A 204 O HOH A 341 1555 1555 3.25 LINK K K A 204 O HOH B 103 1555 1555 2.85 LINK K K A 204 OP2A C b 5 1555 1555 2.71 LINK O HOH A 301 MN B MN b 101 1555 1555 2.10 LINK OP3A C b 5 MN B MN b 101 1555 1555 2.20 LINK OP2 G b 6 MN B MN b 101 1555 1555 2.62 LINK MN B MN b 101 O HOH b 204 1555 1555 2.10 LINK MN B MN b 101 O HOH b 205 1555 1555 2.50 LINK MN B MN b 101 O HOH b 208 1555 1555 2.10 CISPEP 1 ASN A 77 PRO A 78 0 -0.70 SITE 1 AC1 5 ASP A 71 ASP A 192 HOH A 341 C b 5 SITE 2 AC1 5 HOH b 201 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 7 GLU A 122 ASP A 163 GLU A 166 HOH A 332 SITE 2 AC3 7 HOH A 355 HOH A 394 HOH A 396 SITE 1 AC4 3 GLU A 188 HOH B 103 C b 5 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 3 ILE A 64 HOH A 429 HOH A 431 SITE 1 AC7 5 GLU A 66 ARG A 123 SER A 125 LYS A 127 SITE 2 AC7 5 HOH A 304 SITE 1 AC8 7 ARG A 195 HOH A 301 C b 5 G b 6 SITE 2 AC8 7 HOH b 204 HOH b 205 HOH b 208 SITE 1 AC9 4 ASN A 77 DG C 2 DA C 3 HOH C 211 CRYST1 82.013 37.557 61.932 90.00 96.79 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 0.012193 0.000000 0.001452 0.00000 SCALE2 0.000000 0.026626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016261 0.00000