HEADER HYDROLASE/RNA/DNA 09-JUN-18 6DPJ TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 K196A IN TITLE 2 COMPLEX WITH AN RNA/DNA HYBRID: REACTION IN 4 MM MN2+ AND 200 MM K+ TITLE 3 FOR 80 S 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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF INTACT RNA (5'- COMPND 11 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF INTACT RNA (5'- COMPND 16 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 17 CHAIN: b; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 21 CHAIN: C; COMPND 22 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA, BH0863; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 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-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DPJ 1 LINK REVDAT 1 15-AUG-18 6DPJ 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 50779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2458 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 19.4108 - 4.0489 0.93 2629 145 0.1272 0.1648 REMARK 3 2 4.0489 - 3.2185 0.96 2703 146 0.1346 0.1872 REMARK 3 3 3.2185 - 2.8130 0.97 2773 96 0.1697 0.2183 REMARK 3 4 2.8130 - 2.5565 0.98 2803 171 0.1786 0.2400 REMARK 3 5 2.5565 - 2.3736 0.99 2745 157 0.1768 0.2013 REMARK 3 6 2.3736 - 2.2338 0.99 2835 138 0.1828 0.2220 REMARK 3 7 2.2338 - 2.1221 1.00 2857 125 0.1795 0.2172 REMARK 3 8 2.1221 - 2.0298 1.00 2803 152 0.1994 0.2392 REMARK 3 9 2.0298 - 1.9518 1.00 2794 146 0.1995 0.2531 REMARK 3 10 1.9518 - 1.8845 1.00 2807 150 0.2208 0.2686 REMARK 3 11 1.8845 - 1.8256 1.00 2870 138 0.2230 0.2177 REMARK 3 12 1.8256 - 1.7735 1.00 2820 140 0.2216 0.2920 REMARK 3 13 1.7735 - 1.7268 0.99 2783 155 0.2370 0.2703 REMARK 3 14 1.7268 - 1.6847 0.99 2853 138 0.2531 0.2945 REMARK 3 15 1.6847 - 1.6464 0.98 2746 163 0.2645 0.2481 REMARK 3 16 1.6464 - 1.6114 0.92 2601 132 0.2829 0.3428 REMARK 3 17 1.6114 - 1.5792 0.84 2393 111 0.3169 0.3740 REMARK 3 18 1.5792 - 1.5494 0.53 1506 55 0.3208 0.3825 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.96 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 1420 REMARK 3 ANGLE : 1.025 1971 REMARK 3 CHIRALITY : 0.055 217 REMARK 3 PLANARITY : 0.007 206 REMARK 3 DIHEDRAL : 18.481 808 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.570 -4.181 18.969 REMARK 3 T TENSOR REMARK 3 T11: 0.2453 T22: 0.5404 REMARK 3 T33: 0.3709 T12: 0.0690 REMARK 3 T13: 0.0274 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 8.2822 L22: 8.3532 REMARK 3 L33: 5.9757 L12: -0.2047 REMARK 3 L13: -7.0266 L23: 0.4645 REMARK 3 S TENSOR REMARK 3 S11: 0.2408 S12: 0.5184 S13: 0.0213 REMARK 3 S21: -0.3555 S22: -0.0488 S23: -0.7617 REMARK 3 S31: 0.4934 S32: 1.7417 S33: -0.1728 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.589 -6.265 16.834 REMARK 3 T TENSOR REMARK 3 T11: 0.2352 T22: 0.2203 REMARK 3 T33: 0.2381 T12: -0.0080 REMARK 3 T13: 0.0163 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 4.3426 L22: 3.9604 REMARK 3 L33: 6.1028 L12: -2.3620 REMARK 3 L13: 3.1834 L23: -1.6330 REMARK 3 S TENSOR REMARK 3 S11: 0.2415 S12: 0.1397 S13: -0.3591 REMARK 3 S21: -0.0633 S22: -0.0717 S23: 0.2292 REMARK 3 S31: 0.3032 S32: 0.0543 S33: -0.2827 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.710 -11.585 24.104 REMARK 3 T TENSOR REMARK 3 T11: 0.2567 T22: 0.2521 REMARK 3 T33: 0.3523 T12: 0.0433 REMARK 3 T13: 0.0166 T23: 0.0651 REMARK 3 L TENSOR REMARK 3 L11: 2.0694 L22: 8.1122 REMARK 3 L33: 2.2225 L12: -1.5912 REMARK 3 L13: 1.7989 L23: -0.4822 REMARK 3 S TENSOR REMARK 3 S11: 0.3553 S12: 0.0704 S13: -0.8466 REMARK 3 S21: -0.2377 S22: -0.2773 S23: -0.3383 REMARK 3 S31: 0.2962 S32: 0.5173 S33: 0.1046 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.053 -4.921 18.660 REMARK 3 T TENSOR REMARK 3 T11: 0.2787 T22: 0.3368 REMARK 3 T33: 0.3083 T12: -0.0011 REMARK 3 T13: 0.0087 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 6.9747 L22: 5.5715 REMARK 3 L33: 5.7917 L12: -4.2595 REMARK 3 L13: 4.6407 L23: -5.6664 REMARK 3 S TENSOR REMARK 3 S11: -0.0921 S12: -0.3679 S13: -0.5047 REMARK 3 S21: 0.0173 S22: 0.4835 S23: 0.6315 REMARK 3 S31: 0.1218 S32: -0.9654 S33: -0.5163 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.855 0.650 24.010 REMARK 3 T TENSOR REMARK 3 T11: 0.1835 T22: 0.2082 REMARK 3 T33: 0.2146 T12: 0.0000 REMARK 3 T13: 0.0373 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 8.7707 L22: 2.3099 REMARK 3 L33: 4.8645 L12: -2.0953 REMARK 3 L13: 6.5631 L23: -1.1431 REMARK 3 S TENSOR REMARK 3 S11: -0.0586 S12: -0.3005 S13: 0.0003 REMARK 3 S21: 0.0746 S22: -0.0542 S23: 0.0647 REMARK 3 S31: -0.2421 S32: -0.2990 S33: 0.0426 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 123:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.677 -0.915 25.488 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.2084 REMARK 3 T33: 0.2076 T12: 0.0103 REMARK 3 T13: 0.0259 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 6.5681 L22: 2.7204 REMARK 3 L33: 7.2557 L12: -0.7183 REMARK 3 L13: 5.0820 L23: -0.2189 REMARK 3 S TENSOR REMARK 3 S11: -0.0582 S12: -0.2171 S13: -0.0034 REMARK 3 S21: -0.0227 S22: -0.0312 S23: -0.1915 REMARK 3 S31: -0.1279 S32: 0.1263 S33: 0.1127 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.661 9.430 16.751 REMARK 3 T TENSOR REMARK 3 T11: 0.3513 T22: 0.2092 REMARK 3 T33: 0.2901 T12: -0.0523 REMARK 3 T13: 0.0075 T23: 0.0634 REMARK 3 L TENSOR REMARK 3 L11: 9.2129 L22: 7.2342 REMARK 3 L33: 3.3660 L12: -6.8575 REMARK 3 L13: -4.1773 L23: 4.7689 REMARK 3 S TENSOR REMARK 3 S11: 0.0671 S12: 0.0678 S13: 0.4592 REMARK 3 S21: -0.0331 S22: -0.0090 S23: -0.1487 REMARK 3 S31: -0.6079 S32: 0.2112 S33: -0.1134 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.399 7.772 16.125 REMARK 3 T TENSOR REMARK 3 T11: 0.3433 T22: 0.4229 REMARK 3 T33: 0.3227 T12: 0.1972 REMARK 3 T13: 0.0042 T23: -0.1082 REMARK 3 L TENSOR REMARK 3 L11: 6.0476 L22: 1.8357 REMARK 3 L33: 5.1223 L12: -0.2891 REMARK 3 L13: 0.4999 L23: -1.5654 REMARK 3 S TENSOR REMARK 3 S11: -0.1477 S12: -0.0097 S13: 0.5052 REMARK 3 S21: -0.5275 S22: -0.3158 S23: 0.4850 REMARK 3 S31: -0.6701 S32: -0.9909 S33: 0.2059 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.117 5.772 24.948 REMARK 3 T TENSOR REMARK 3 T11: 0.2788 T22: 0.3650 REMARK 3 T33: 0.2643 T12: 0.0664 REMARK 3 T13: 0.0345 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 5.3890 L22: 8.6769 REMARK 3 L33: 4.4578 L12: 4.4008 REMARK 3 L13: 4.8063 L23: 4.9585 REMARK 3 S TENSOR REMARK 3 S11: 0.3569 S12: -0.4066 S13: 0.0346 REMARK 3 S21: 0.2080 S22: -0.4342 S23: 0.1818 REMARK 3 S31: -0.1372 S32: -0.7984 S33: 0.2564 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.184 8.427 30.372 REMARK 3 T TENSOR REMARK 3 T11: 0.3280 T22: 0.2779 REMARK 3 T33: 0.2778 T12: -0.0162 REMARK 3 T13: 0.0056 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 4.8997 L22: 4.2114 REMARK 3 L33: 6.5734 L12: -1.1453 REMARK 3 L13: -4.6237 L23: 4.0197 REMARK 3 S TENSOR REMARK 3 S11: 0.3862 S12: -0.3778 S13: 0.3299 REMARK 3 S21: -0.4007 S22: 0.0479 S23: -0.3734 REMARK 3 S31: -0.7582 S32: 0.4307 S33: -0.3760 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.318 -0.857 12.358 REMARK 3 T TENSOR REMARK 3 T11: 0.3448 T22: 0.4550 REMARK 3 T33: 0.2733 T12: 0.0960 REMARK 3 T13: 0.0575 T23: 0.0651 REMARK 3 L TENSOR REMARK 3 L11: 3.0182 L22: 4.8837 REMARK 3 L33: 4.9941 L12: -1.3529 REMARK 3 L13: -0.2836 L23: 4.8009 REMARK 3 S TENSOR REMARK 3 S11: 0.5324 S12: 0.8462 S13: 0.1297 REMARK 3 S21: -0.3707 S22: -0.5744 S23: -0.5729 REMARK 3 S31: 0.0506 S32: 0.4132 S33: -0.0267 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.612 -9.289 13.069 REMARK 3 T TENSOR REMARK 3 T11: 0.4038 T22: 0.3072 REMARK 3 T33: 0.2524 T12: 0.0476 REMARK 3 T13: 0.0063 T23: -0.0610 REMARK 3 L TENSOR REMARK 3 L11: 5.5004 L22: 4.4420 REMARK 3 L33: 9.8172 L12: -0.4371 REMARK 3 L13: -7.0990 L23: -1.1271 REMARK 3 S TENSOR REMARK 3 S11: -0.2131 S12: 0.8017 S13: -0.4864 REMARK 3 S21: -0.4576 S22: -0.0789 S23: 0.1236 REMARK 3 S31: 0.8920 S32: -0.5276 S33: 0.1523 REMARK 3 TLS GROUP : 13 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): 23.630 1.393 4.688 REMARK 3 T TENSOR REMARK 3 T11: 0.3569 T22: 0.3398 REMARK 3 T33: 0.2187 T12: 0.0403 REMARK 3 T13: 0.0512 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 2.8671 L22: 9.0903 REMARK 3 L33: 2.4808 L12: 0.2211 REMARK 3 L13: 2.1169 L23: -1.2477 REMARK 3 S TENSOR REMARK 3 S11: -0.0433 S12: 0.5402 S13: -0.1394 REMARK 3 S21: -0.6576 S22: -0.1538 S23: -0.2594 REMARK 3 S31: 0.2077 S32: 0.2101 S33: 0.1617 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.353 3.856 3.226 REMARK 3 T TENSOR REMARK 3 T11: 0.4687 T22: 0.2837 REMARK 3 T33: 0.2591 T12: 0.0558 REMARK 3 T13: -0.0587 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 1.9142 L22: 7.0602 REMARK 3 L33: 5.0853 L12: -1.9775 REMARK 3 L13: -2.8492 L23: 4.8618 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: 0.1279 S13: -0.1958 REMARK 3 S21: -0.7950 S22: -0.3334 S23: 0.1206 REMARK 3 S31: -0.5344 S32: -0.2530 S33: 0.5623 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 6DPJ 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_1000235035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-15 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 : 26181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 19.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 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 40.94200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.77450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.94200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.77450 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: 4710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 A 390 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 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 ARG A 195 REMARK 465 ALA 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: 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 104 O HOH B 108 2.18 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 DG C 2 O3' DG C 2 C3' -0.043 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 404 DISTANCE = 6.22 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 98.1 REMARK 620 3 HOH A 317 O 84.9 83.1 REMARK 620 4 HOH A 337 O 90.9 93.7 174.3 REMARK 620 5 C b 5 OP1 93.2 168.5 96.2 87.8 REMARK 620 6 HOH b 101 O 171.7 83.7 87.3 97.0 84.8 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 102.1 REMARK 620 3 ASP A 132 OD1 127.2 94.3 REMARK 620 4 ASP A 132 OD2 104.3 147.7 54.7 REMARK 620 5 U B 4 O3' 145.3 82.6 86.0 86.2 REMARK 620 6 C b 5 OP1 88.6 111.0 131.2 88.0 58.3 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 TYR A 193 O 77.4 REMARK 620 3 HOH A 317 O 53.0 93.0 REMARK 620 4 HOH A 345 O 65.1 107.0 107.9 REMARK 620 5 G b 6 OP2 101.4 130.2 53.9 117.5 REMARK 620 6 HOH b 101 O 57.8 135.1 59.1 58.5 63.3 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 DT C 4 O4 REMARK 620 2 DG C 5 O6 71.4 REMARK 620 3 HOH C 208 O 83.5 79.1 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 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 EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 K C 101 DBREF 6DPJ A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DPJ B 1 4 PDB 6DPJ 6DPJ 1 4 DBREF 6DPJ b 5 6 PDB 6DPJ 6DPJ 5 6 DBREF 6DPJ C 1 6 PDB 6DPJ 6DPJ 1 6 SEQADV 6DPJ GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPJ SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPJ HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPJ MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPJ ALA A 196 UNP Q9KEI9 LYS 196 ENGINEERED MUTATION 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 ALA 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 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 EDO A 208 4 HET EDO A 209 4 HET GOL A 210 6 HET K C 101 1 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MN 2(MN 2+) FORMUL 7 K 2(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 EDO 2(C2 H6 O2) FORMUL 14 GOL C3 H8 O3 FORMUL 16 HOH *130(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 ASN A 152 GLU A 154 5 3 HELIX 4 AA4 THR A 155 ASN A 170 1 16 HELIX 5 AA5 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 1.59 LINK OD2 ASP A 71 MN MN A 201 1555 1555 2.13 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.04 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.04 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.12 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.57 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.11 LINK OD1 ASP A 192 K K A 203 1555 1555 3.12 LINK O TYR A 193 K K A 203 1555 1555 2.45 LINK MN MN A 201 O HOH A 317 1555 1555 2.20 LINK MN MN A 201 O HOH A 337 1555 1555 2.22 LINK MN MN A 201 OP1 C b 5 1555 1555 2.28 LINK MN MN A 201 O HOH b 101 1555 1555 2.16 LINK MN MN A 202 O3' U B 4 1555 1555 2.62 LINK MN MN A 202 OP1 C b 5 1555 1555 2.25 LINK K K A 203 O HOH A 317 1555 1555 3.28 LINK K K A 203 O HOH A 345 1555 1555 2.71 LINK K K A 203 OP2 G b 6 1555 1555 2.89 LINK K K A 203 O HOH b 101 1555 1555 2.75 LINK O4 DT C 4 K A K C 101 1555 1555 3.33 LINK O6 DG C 5 K A K C 101 1555 1555 2.59 LINK K A K C 101 O HOH C 208 1555 1555 3.18 CISPEP 1 ASN A 77 PRO A 78 0 2.29 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 317 HOH A 337 SITE 2 AC1 6 C b 5 HOH b 101 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 5 ASP A 192 TYR A 193 HOH A 345 G b 6 SITE 2 AC3 5 HOH b 101 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 2 HOH A 387 HOH A 404 SITE 1 AC6 1 HIS A 172 SITE 1 AC7 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AC8 5 GLY A 73 SER A 74 GLN A 75 ILE A 80 SITE 2 AC8 5 GLU A 82 SITE 1 AC9 7 GLY A 76 ASN A 77 PRO A 78 A B 1 SITE 2 AC9 7 DG C 2 DA C 3 G b 6 SITE 1 AD1 3 DT C 4 DG C 5 HOH C 211 CRYST1 81.884 37.549 62.400 90.00 97.23 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 0.012212 0.000000 0.001549 0.00000 SCALE2 0.000000 0.026632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016154 0.00000