HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DPF TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 40 MM MN2+ AND 200 MM K+ FOR 40 S TITLE 3 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') PORTION OF CLEAVED RNA; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3') PORTION OF CLEAVED RNA; 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; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC; 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 6DPF 1 LINK REVDAT 1 15-AUG-18 6DPF 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. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 25946 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1285 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 19.9253 - 3.2331 0.96 2802 140 0.1257 0.1675 REMARK 3 2 3.2331 - 2.5679 0.98 2762 166 0.1597 0.2156 REMARK 3 3 2.5679 - 2.2438 0.99 2790 146 0.1695 0.2135 REMARK 3 4 2.2438 - 2.0389 0.99 2771 153 0.1713 0.1991 REMARK 3 5 2.0389 - 1.8929 0.99 2795 133 0.1877 0.2361 REMARK 3 6 1.8929 - 1.7813 0.99 2785 147 0.2209 0.2596 REMARK 3 7 1.7813 - 1.6922 0.98 2756 144 0.2307 0.2557 REMARK 3 8 1.6922 - 1.6186 0.98 2743 143 0.2524 0.2890 REMARK 3 9 1.6186 - 1.5563 0.87 2457 113 0.2725 0.3061 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) : 22.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.94 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 1466 REMARK 3 ANGLE : 1.044 2020 REMARK 3 CHIRALITY : 0.056 219 REMARK 3 PLANARITY : 0.006 211 REMARK 3 DIHEDRAL : 18.948 831 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): 40.8951 -4.1477 18.2881 REMARK 3 T TENSOR REMARK 3 T11: 0.3056 T22: 0.6339 REMARK 3 T33: 0.3732 T12: 0.0594 REMARK 3 T13: 0.0348 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 2.6881 L22: 4.2562 REMARK 3 L33: 7.4674 L12: 0.5427 REMARK 3 L13: -3.2227 L23: -3.9201 REMARK 3 S TENSOR REMARK 3 S11: 0.3035 S12: 0.4177 S13: -0.0319 REMARK 3 S21: -0.4550 S22: -0.6194 S23: -1.0680 REMARK 3 S31: -0.2266 S32: 2.5038 S33: 0.3786 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5265 -6.2607 16.0512 REMARK 3 T TENSOR REMARK 3 T11: 0.2131 T22: 0.2218 REMARK 3 T33: 0.1705 T12: 0.0167 REMARK 3 T13: -0.0171 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 5.2866 L22: 1.1623 REMARK 3 L33: 4.1701 L12: -0.6307 REMARK 3 L13: 4.7437 L23: -0.5533 REMARK 3 S TENSOR REMARK 3 S11: 0.1899 S12: 0.2275 S13: -0.4202 REMARK 3 S21: -0.1268 S22: -0.0716 S23: 0.0469 REMARK 3 S31: 0.1996 S32: 0.0335 S33: -0.2482 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2380 -11.5942 23.4419 REMARK 3 T TENSOR REMARK 3 T11: 0.2929 T22: 0.2097 REMARK 3 T33: 0.3458 T12: 0.0839 REMARK 3 T13: -0.0288 T23: 0.0408 REMARK 3 L TENSOR REMARK 3 L11: 6.2934 L22: 5.5393 REMARK 3 L33: 8.4555 L12: -0.6797 REMARK 3 L13: -6.9194 L23: 0.9269 REMARK 3 S TENSOR REMARK 3 S11: -0.1756 S12: -0.0328 S13: -1.6196 REMARK 3 S21: 0.1826 S22: -0.0222 S23: -0.2314 REMARK 3 S31: 0.7318 S32: 0.3518 S33: 0.2593 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5097 -4.9318 18.2303 REMARK 3 T TENSOR REMARK 3 T11: 0.2530 T22: 0.3204 REMARK 3 T33: 0.2148 T12: -0.0203 REMARK 3 T13: -0.0200 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 4.3132 L22: 5.7592 REMARK 3 L33: 6.4332 L12: -1.9033 REMARK 3 L13: 2.0349 L23: -6.0843 REMARK 3 S TENSOR REMARK 3 S11: -0.0073 S12: -0.3610 S13: -0.1680 REMARK 3 S21: -0.1656 S22: 0.4330 S23: 0.3866 REMARK 3 S31: 0.2860 S32: -1.0747 S33: -0.4941 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3298 0.5841 23.5928 REMARK 3 T TENSOR REMARK 3 T11: 0.1399 T22: 0.1578 REMARK 3 T33: 0.1715 T12: -0.0063 REMARK 3 T13: 0.0200 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 6.6274 L22: 2.8601 REMARK 3 L33: 7.7056 L12: -1.3857 REMARK 3 L13: 5.3913 L23: -0.3020 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: -0.1394 S13: -0.0046 REMARK 3 S21: 0.0684 S22: -0.0803 S23: 0.0399 REMARK 3 S31: -0.1566 S32: -0.2045 S33: 0.0537 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 123:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9527 3.6702 21.1197 REMARK 3 T TENSOR REMARK 3 T11: 0.1587 T22: 0.1590 REMARK 3 T33: 0.1697 T12: -0.0486 REMARK 3 T13: 0.0261 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 4.6753 L22: 1.9627 REMARK 3 L33: 6.6834 L12: -1.8592 REMARK 3 L13: 2.8333 L23: -0.0778 REMARK 3 S TENSOR REMARK 3 S11: 0.0985 S12: 0.0959 S13: 0.2014 REMARK 3 S21: -0.0923 S22: -0.1005 S23: -0.1500 REMARK 3 S31: -0.2163 S32: 0.1903 S33: -0.0006 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3325 9.5529 15.7203 REMARK 3 T TENSOR REMARK 3 T11: 0.4308 T22: 0.4217 REMARK 3 T33: 0.2839 T12: 0.2176 REMARK 3 T13: -0.0300 T23: -0.0675 REMARK 3 L TENSOR REMARK 3 L11: 3.6843 L22: 1.7597 REMARK 3 L33: 5.1711 L12: 2.0469 REMARK 3 L13: 3.5446 L23: 0.8515 REMARK 3 S TENSOR REMARK 3 S11: -0.1686 S12: -0.0948 S13: 0.7050 REMARK 3 S21: -0.2793 S22: -0.3794 S23: 0.5346 REMARK 3 S31: -0.8400 S32: -0.7114 S33: 0.3962 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 153:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4778 5.0220 23.0046 REMARK 3 T TENSOR REMARK 3 T11: 0.2092 T22: 0.3528 REMARK 3 T33: 0.2054 T12: 0.0553 REMARK 3 T13: 0.0198 T23: -0.0582 REMARK 3 L TENSOR REMARK 3 L11: 5.0841 L22: 5.4403 REMARK 3 L33: 6.1548 L12: 0.1227 REMARK 3 L13: 3.6439 L23: 0.2801 REMARK 3 S TENSOR REMARK 3 S11: 0.1702 S12: -0.3117 S13: 0.0046 REMARK 3 S21: -0.0540 S22: -0.3541 S23: 0.4554 REMARK 3 S31: -0.0007 S32: -0.9139 S33: 0.1929 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.6776 8.3106 29.8828 REMARK 3 T TENSOR REMARK 3 T11: 0.2301 T22: 0.2100 REMARK 3 T33: 0.2119 T12: -0.0099 REMARK 3 T13: 0.0116 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 6.1904 L22: 4.2813 REMARK 3 L33: 5.1123 L12: -4.2818 REMARK 3 L13: -1.5744 L23: 3.6006 REMARK 3 S TENSOR REMARK 3 S11: 0.0995 S12: -0.4618 S13: 0.4387 REMARK 3 S21: -0.0731 S22: 0.2080 S23: -0.3936 REMARK 3 S31: -0.3639 S32: 0.4174 S33: -0.3088 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5827 -0.8271 11.8640 REMARK 3 T TENSOR REMARK 3 T11: 0.2827 T22: 0.3491 REMARK 3 T33: 0.2096 T12: 0.0620 REMARK 3 T13: 0.0476 T23: 0.0357 REMARK 3 L TENSOR REMARK 3 L11: 1.9910 L22: 4.9444 REMARK 3 L33: 5.0948 L12: 0.1744 REMARK 3 L13: 1.2735 L23: 4.7244 REMARK 3 S TENSOR REMARK 3 S11: 0.2442 S12: 0.3959 S13: 0.0320 REMARK 3 S21: -0.4613 S22: -0.1497 S23: -0.4839 REMARK 3 S31: 0.0535 S32: 0.4576 S33: -0.0268 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2947 -9.5888 11.0867 REMARK 3 T TENSOR REMARK 3 T11: 0.2806 T22: 0.2506 REMARK 3 T33: 0.2223 T12: 0.0953 REMARK 3 T13: -0.0323 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 4.5329 L22: 8.6080 REMARK 3 L33: 7.9037 L12: 4.9683 REMARK 3 L13: -1.6670 L23: 2.9848 REMARK 3 S TENSOR REMARK 3 S11: -0.0543 S12: 0.3700 S13: -0.0707 REMARK 3 S21: -0.2734 S22: 0.0810 S23: 0.3015 REMARK 3 S31: 0.2278 S32: 0.1248 S33: -0.0317 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): 23.9495 1.2478 4.2840 REMARK 3 T TENSOR REMARK 3 T11: 0.3011 T22: 0.3335 REMARK 3 T33: 0.1660 T12: 0.0906 REMARK 3 T13: 0.0438 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.9236 L22: 6.8496 REMARK 3 L33: 3.7411 L12: -1.9572 REMARK 3 L13: 2.5089 L23: -1.1516 REMARK 3 S TENSOR REMARK 3 S11: 0.1092 S12: 0.3288 S13: 0.1736 REMARK 3 S21: -0.5850 S22: -0.3738 S23: -0.3432 REMARK 3 S31: 0.0013 S32: 0.1947 S33: 0.2756 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4946 3.5979 2.9387 REMARK 3 T TENSOR REMARK 3 T11: 0.4773 T22: 0.3225 REMARK 3 T33: 0.1791 T12: 0.0837 REMARK 3 T13: -0.0555 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.6105 L22: 4.4713 REMARK 3 L33: 3.7374 L12: -0.8279 REMARK 3 L13: -2.2549 L23: 2.6758 REMARK 3 S TENSOR REMARK 3 S11: -0.0395 S12: 0.1891 S13: -0.0474 REMARK 3 S21: -0.8686 S22: -0.2723 S23: 0.2470 REMARK 3 S31: -0.7843 S32: -0.2366 S33: 0.3174 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES REFINED IN PHENIX AND REMARK 3 NUCLEIC ACID AND PROTEIN RESIDUES BUILT IN COOT REMARK 4 REMARK 4 6DPF 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_1000235010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-16 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 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.6 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: PHENIX REMARK 200 STARTING MODEL: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 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 40.86300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.80500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.86300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.80500 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: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 THE RNA CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) 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 A 409 O HOH A 422 2.02 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 -0.096 REMARK 500 DG C 2 O3' DG C 2 C3' -0.042 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 C b 5 N3 - C4 - C5 ANGL. DEV. = -2.5 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 441 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 442 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 443 DISTANCE = 6.63 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 111.9 REMARK 620 3 HOH A 330 O 89.1 88.1 REMARK 620 4 HOH A 343 O 86.2 85.5 170.0 REMARK 620 5 C b 5 OP3 154.8 93.4 92.1 95.9 REMARK 620 6 C b 5 OP1 93.8 153.0 83.9 105.2 61.3 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 96.0 REMARK 620 3 ASP A 132 OD1 132.8 95.5 REMARK 620 4 ASP A 132 OD2 101.9 150.3 55.1 REMARK 620 5 C b 5 OP1 98.5 111.0 119.4 89.8 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 97.5 REMARK 620 3 HOH A 320 O 171.8 85.9 REMARK 620 4 HOH A 331 O 96.9 89.5 90.5 REMARK 620 5 HOH A 381 O 98.6 163.6 77.7 91.6 REMARK 620 6 HOH A 395 O 86.6 91.6 85.8 176.1 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 217 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 HOH A 330 O 51.7 REMARK 620 3 HOH A 365 O 63.7 55.9 REMARK 620 4 HOH B 206 O 119.7 170.0 127.6 REMARK 620 5 C b 5 OP2 109.1 78.8 127.8 101.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 196 O REMARK 620 2 HOH A 398 O 83.0 REMARK 620 3 HOH C 101 O 86.1 82.0 REMARK 620 4 HOH C 106 O 172.8 102.6 90.2 REMARK 620 N 1 2 3 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 G b 6 O6 REMARK 620 2 HOH b 203 O 95.1 REMARK 620 3 HOH C 104 O 94.1 167.9 REMARK 620 N 1 2 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 MN 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 GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN b 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD b 102 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RNA CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) AT THE POSITION 4- REMARK 999 5, WHERE THE CLEAVAGE OCCURS DBREF 6DPF A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DPF B 1 4 PDB 6DPF 6DPF 1 4 DBREF 6DPF b 5 6 PDB 6DPF 6DPF 5 6 DBREF 6DPF C 1 6 PDB 6DPF 6DPF 1 6 SEQRES 1 A 136 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 136 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 136 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 136 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 136 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 136 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 136 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 136 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 136 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 136 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 136 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 MN A 201 1 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET IOD A 208 1 HET GOL A 209 6 HET GOL A 210 6 HET EDO A 211 4 HET GOL A 212 6 HET EDO A 213 4 HET EDO A 214 4 HET EDO A 215 4 HET PGE A 216 10 HET K A 217 1 HET MN b 101 1 HET IOD b 102 1 HETNAM MN MANGANESE (II) ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 5(MN 2+) FORMUL 9 IOD 5(I 1-) FORMUL 13 GOL 3(C3 H8 O3) FORMUL 15 EDO 4(C2 H6 O2) FORMUL 20 PGE C6 H14 O4 FORMUL 21 K K 1+ FORMUL 24 HOH *167(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 OD2 ASP A 71 MN MN A 201 1555 1555 2.04 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.07 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.04 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.00 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.57 LINK OD1 ASP A 163 MN MN A 203 1555 1555 2.26 LINK OE1 GLU A 166 MN MN A 203 1555 1555 2.06 LINK OE2 GLU A 188 K K A 217 1555 1555 2.99 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.10 LINK O LYS A 196 MN MN A 204 1555 1555 2.22 LINK MN MN A 201 O HOH A 330 1555 1555 2.16 LINK MN MN A 201 O HOH A 343 1555 1555 2.08 LINK MN MN A 201 OP3 C b 5 1555 1555 2.15 LINK MN MN A 201 OP1 C b 5 1555 1555 2.53 LINK MN MN A 202 OP1 C b 5 1555 1555 2.03 LINK MN MN A 203 O HOH A 320 1555 4556 2.03 LINK MN MN A 203 O HOH A 331 1555 1555 2.40 LINK MN MN A 203 O HOH A 381 1555 4556 2.22 LINK MN MN A 203 O HOH A 395 1555 1555 2.11 LINK MN MN A 204 O HOH A 398 1555 1555 2.66 LINK MN MN A 204 O HOH C 101 1555 4545 2.18 LINK MN MN A 204 O HOH C 106 1555 4545 2.13 LINK K K A 217 O HOH A 330 1555 1555 3.37 LINK K K A 217 O HOH A 365 1555 1555 3.34 LINK K K A 217 O HOH B 206 1555 1555 2.70 LINK K K A 217 OP2 C b 5 1555 1555 2.67 LINK O6 G b 6 MN MN b 101 1555 1555 2.79 LINK MN MN b 101 O HOH b 203 1555 1555 2.41 LINK MN MN b 101 O HOH C 104 1555 4545 2.22 CISPEP 1 ASN A 77 PRO A 78 0 1.01 SITE 1 AC1 5 ASP A 71 ASP A 192 HOH A 330 HOH A 343 SITE 2 AC1 5 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 163 GLU A 166 HOH A 320 HOH A 331 SITE 2 AC3 6 HOH A 381 HOH A 395 SITE 1 AC4 5 LYS A 196 HOH A 398 HOH C 101 HOH C 104 SITE 2 AC4 5 HOH C 106 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 3 ILE A 64 HOH A 410 HOH A 443 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 314 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 7 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AC8 7 ASN A 170 GOL A 212 HOH A 323 SITE 1 AC9 3 THR A 148 DT C 4 DG C 5 SITE 1 AD1 5 HIS A 115 ARG A 118 ASN A 170 GOL A 210 SITE 2 AD1 5 HOH A 301 SITE 1 AD2 3 THR A 173 TYR A 174 HOH A 308 SITE 1 AD3 3 GLU A 66 LEU A 94 LYS A 127 SITE 1 AD4 5 GLU A 61 GLU A 62 ILE A 63 TRP A 65 SITE 2 AD4 5 HOH A 405 SITE 1 AD5 8 ILE A 102 THR A 148 LEU A 149 VAL A 150 SITE 2 AD5 8 ASN A 152 GLU A 154 HOH A 307 HOH C 108 SITE 1 AD6 4 GLU A 188 U B 4 HOH B 206 C b 5 SITE 1 AD7 3 HOH C 104 G b 6 HOH b 203 SITE 1 AD8 1 HOH A 391 CRYST1 81.726 37.610 61.195 90.00 96.20 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 0.012236 0.000000 0.001329 0.00000 SCALE2 0.000000 0.026589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016437 0.00000