HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DPA TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 4 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 6DPA 1 LINK REVDAT 1 15-AUG-18 6DPA 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. 1.49 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 30229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1530 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 19.8290 - 3.3071 0.99 2756 124 0.1285 0.1577 REMARK 3 2 3.3071 - 2.6269 1.00 2676 150 0.1483 0.1676 REMARK 3 3 2.6269 - 2.2954 0.99 2647 153 0.1509 0.1753 REMARK 3 4 2.2954 - 2.0857 0.99 2617 144 0.1453 0.1988 REMARK 3 5 2.0857 - 1.9364 0.99 2631 136 0.1566 0.1853 REMARK 3 6 1.9364 - 1.8223 0.99 2596 164 0.1766 0.2002 REMARK 3 7 1.8223 - 1.7311 0.98 2584 138 0.1860 0.2449 REMARK 3 8 1.7311 - 1.6558 0.97 2597 112 0.1987 0.2388 REMARK 3 9 1.6558 - 1.5921 0.97 2604 142 0.2196 0.2532 REMARK 3 10 1.5921 - 1.5372 0.97 2536 142 0.2444 0.2712 REMARK 3 11 1.5372 - 1.4891 0.93 2455 125 0.2898 0.2971 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.82 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 : 1.083 2030 REMARK 3 CHIRALITY : 0.073 225 REMARK 3 PLANARITY : 0.006 209 REMARK 3 DIHEDRAL : 22.769 583 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0698 -5.8495 17.0932 REMARK 3 T TENSOR REMARK 3 T11: 0.1825 T22: 0.1815 REMARK 3 T33: 0.1366 T12: 0.0149 REMARK 3 T13: 0.0335 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 3.5476 L22: 1.6504 REMARK 3 L33: 2.6405 L12: -0.8997 REMARK 3 L13: 1.8847 L23: 0.1015 REMARK 3 S TENSOR REMARK 3 S11: 0.2732 S12: 0.3710 S13: -0.1482 REMARK 3 S21: -0.1366 S22: -0.1947 S23: -0.1264 REMARK 3 S31: 0.3098 S32: 0.3214 S33: -0.0527 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0489 -11.5112 23.9184 REMARK 3 T TENSOR REMARK 3 T11: 0.2688 T22: 0.1981 REMARK 3 T33: 0.3287 T12: 0.0636 REMARK 3 T13: 0.0243 T23: 0.0687 REMARK 3 L TENSOR REMARK 3 L11: 5.8838 L22: 8.4504 REMARK 3 L33: 6.8073 L12: -1.7325 REMARK 3 L13: -5.7730 L23: 1.8491 REMARK 3 S TENSOR REMARK 3 S11: -0.0607 S12: -0.5230 S13: -1.0015 REMARK 3 S21: -0.0069 S22: 0.0129 S23: -0.8400 REMARK 3 S31: 0.7101 S32: 0.4656 S33: 0.1704 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4467 -5.0857 18.5733 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.2885 REMARK 3 T33: 0.1672 T12: -0.0314 REMARK 3 T13: 0.0037 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 2.3289 L22: 6.0944 REMARK 3 L33: 5.9280 L12: -3.4680 REMARK 3 L13: 3.6416 L23: -5.3191 REMARK 3 S TENSOR REMARK 3 S11: 0.1290 S12: -0.4717 S13: -0.4635 REMARK 3 S21: -0.0510 S22: 0.3000 S23: 0.4682 REMARK 3 S31: 0.2070 S32: -0.8918 S33: -0.4819 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5942 2.1205 22.5749 REMARK 3 T TENSOR REMARK 3 T11: 0.1427 T22: 0.0901 REMARK 3 T33: 0.1178 T12: -0.0048 REMARK 3 T13: 0.0447 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 4.1630 L22: 1.3286 REMARK 3 L33: 3.9540 L12: -1.0971 REMARK 3 L13: 2.4590 L23: -0.0016 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: -0.0620 S13: 0.1174 REMARK 3 S21: -0.0391 S22: -0.0537 S23: -0.0339 REMARK 3 S31: -0.1762 S32: -0.0336 S33: -0.0053 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 142:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5595 7.9265 16.3695 REMARK 3 T TENSOR REMARK 3 T11: 0.3383 T22: 0.3596 REMARK 3 T33: 0.2165 T12: 0.2115 REMARK 3 T13: -0.0071 T23: -0.1120 REMARK 3 L TENSOR REMARK 3 L11: 8.1125 L22: 3.5667 REMARK 3 L33: 5.3553 L12: 1.2654 REMARK 3 L13: 1.5383 L23: 0.8408 REMARK 3 S TENSOR REMARK 3 S11: 0.2974 S12: -0.0048 S13: 0.4167 REMARK 3 S21: -0.1424 S22: -0.6212 S23: 0.5112 REMARK 3 S31: -0.6916 S32: -1.0651 S33: 0.2438 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3547 5.7013 24.8585 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.2235 REMARK 3 T33: 0.1500 T12: 0.0547 REMARK 3 T13: 0.0295 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 7.8557 L22: 1.8125 REMARK 3 L33: 8.5754 L12: 1.6444 REMARK 3 L13: 6.4676 L23: 2.7288 REMARK 3 S TENSOR REMARK 3 S11: 0.1648 S12: -0.3093 S13: -0.0902 REMARK 3 S21: -0.0352 S22: -0.2073 S23: 0.1187 REMARK 3 S31: -0.2226 S32: -0.7248 S33: 0.1145 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3717 8.4226 30.2990 REMARK 3 T TENSOR REMARK 3 T11: 0.1987 T22: 0.1837 REMARK 3 T33: 0.1839 T12: -0.0087 REMARK 3 T13: 0.0328 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 4.7505 L22: 4.9700 REMARK 3 L33: 6.6440 L12: -4.8400 REMARK 3 L13: -5.6062 L23: 5.7288 REMARK 3 S TENSOR REMARK 3 S11: 0.1723 S12: -0.4002 S13: 0.6990 REMARK 3 S21: -0.2191 S22: 0.1979 S23: -0.5049 REMARK 3 S31: -0.3497 S32: 0.4159 S33: -0.2964 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.4906 -0.6842 12.2962 REMARK 3 T TENSOR REMARK 3 T11: 0.3068 T22: 0.3735 REMARK 3 T33: 0.1846 T12: 0.1049 REMARK 3 T13: 0.0903 T23: 0.0455 REMARK 3 L TENSOR REMARK 3 L11: 2.1477 L22: 6.8459 REMARK 3 L33: 3.6070 L12: 0.8168 REMARK 3 L13: 0.0130 L23: 4.4277 REMARK 3 S TENSOR REMARK 3 S11: 0.1878 S12: 0.6510 S13: -0.0598 REMARK 3 S21: -0.7206 S22: -0.2124 S23: -0.5138 REMARK 3 S31: 0.1454 S32: 0.6043 S33: -0.1128 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0473 -8.0429 12.0106 REMARK 3 T TENSOR REMARK 3 T11: 0.3849 T22: 0.3562 REMARK 3 T33: 0.2149 T12: 0.0157 REMARK 3 T13: 0.0279 T23: -0.0629 REMARK 3 L TENSOR REMARK 3 L11: 2.3821 L22: 1.4495 REMARK 3 L33: 1.3406 L12: 0.8884 REMARK 3 L13: -1.2295 L23: -0.3004 REMARK 3 S TENSOR REMARK 3 S11: -0.0247 S12: 0.6012 S13: -0.1745 REMARK 3 S21: -0.3728 S22: 0.0776 S23: 0.2327 REMARK 3 S31: 0.8612 S32: -0.2134 S33: 0.2283 REMARK 3 TLS GROUP : 10 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): 23.6990 0.8719 4.9703 REMARK 3 T TENSOR REMARK 3 T11: 0.2933 T22: 0.2301 REMARK 3 T33: 0.1296 T12: 0.0626 REMARK 3 T13: 0.0636 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 3.8742 L22: 7.7082 REMARK 3 L33: 3.1457 L12: -0.5793 REMARK 3 L13: 3.3277 L23: -0.5480 REMARK 3 S TENSOR REMARK 3 S11: -0.0384 S12: 0.4868 S13: 0.0105 REMARK 3 S21: -0.7144 S22: -0.1631 S23: -0.3531 REMARK 3 S31: 0.0188 S32: 0.2203 S33: 0.2403 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3614 3.5669 3.1858 REMARK 3 T TENSOR REMARK 3 T11: 0.4192 T22: 0.2002 REMARK 3 T33: 0.1528 T12: 0.0871 REMARK 3 T13: -0.0144 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.6295 L22: 1.8634 REMARK 3 L33: 9.2731 L12: -1.4766 REMARK 3 L13: -1.4231 L23: 3.2158 REMARK 3 S TENSOR REMARK 3 S11: 0.0758 S12: 0.2979 S13: -0.1403 REMARK 3 S21: -0.7941 S22: -0.3841 S23: 0.0502 REMARK 3 S31: -0.4174 S32: -0.2660 S33: 0.3192 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 6DPA 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_1000235013. 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 : 30236 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 19.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 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 (%): 50.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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 40.59950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.87300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.59950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.87300 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: 5380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 450 REMARK 450 SOURCE REMARK 450 THE RNA CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) AT THE POSITION 4- REMARK 450 5, WHERE THE CLEAVAGE OCCURS 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 ARG A 195 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: 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 O1 GOL A 208 O HOH A 301 2.08 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 -0.135 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 U B 4 O5' - P - OP1 ANGL. DEV. = 8.4 DEGREES REMARK 500 U B 4 O5' - P - OP2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.2 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 436 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 437 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A 438 DISTANCE = 7.48 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 108.8 REMARK 620 3 HOH A 305 O 165.1 65.5 REMARK 620 4 HOH A 315 O 93.4 98.7 74.5 REMARK 620 5 HOH A 318 O 87.7 87.5 105.4 172.9 REMARK 620 6 C b 5 OP3 161.2 89.9 27.4 81.4 95.2 REMARK 620 7 C b 5 OP1 98.5 150.7 90.3 89.8 83.1 63.6 REMARK 620 8 C b 5 OP1 104.6 142.4 85.6 95.9 77.1 58.3 8.9 REMARK 620 N 1 2 3 4 5 6 7 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 101.4 REMARK 620 3 ASP A 132 OD1 140.7 88.8 REMARK 620 4 ASP A 132 OD2 114.5 139.3 51.3 REMARK 620 5 C b 5 OP1 90.3 106.2 123.4 92.7 REMARK 620 6 C b 5 OP1 91.4 113.4 119.3 85.2 7.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 214 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HOH A 346 O 50.0 REMARK 620 3 HOH B 206 O 149.3 110.7 REMARK 620 4 C b 5 OP2 95.0 129.6 114.0 REMARK 620 N 1 2 3 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 HOH A 305 O 45.5 REMARK 620 3 HOH A 315 O 51.9 46.0 REMARK 620 4 G b 6 OP2 91.3 53.7 48.6 REMARK 620 N 1 2 3 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 77.7 REMARK 620 3 HOH C 211 O 88.1 82.4 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 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 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 EDO 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 K A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 DBREF 6DPA A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DPA B 1 4 PDB 6DPA 6DPA 1 4 DBREF 6DPA b 5 6 PDB 6DPA 6DPA 5 6 DBREF 6DPA C 1 6 PDB 6DPA 6DPA 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 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 EDO A 211 4 HET EDO A 212 4 HET EDO A 213 4 HET K A 214 1 HET K C 101 1 HETNAM MN MANGANESE (II) 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 MN 2(MN 2+) FORMUL 7 K 3(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 3(C3 H8 O3) FORMUL 15 EDO 3(C2 H6 O2) FORMUL 20 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 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'C U B 4 P C C b 5 1555 1555 1.59 LINK OD2 ASP A 71 MN MN A 201 1555 1555 1.99 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.05 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.26 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.34 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.68 LINK OD2 ASP A 132 K B K A 214 1555 1555 3.29 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.01 LINK OD1 ASP A 192 K C K A 203 1555 1555 3.21 LINK MN MN A 201 O CHOH A 305 1555 1555 2.27 LINK MN MN A 201 O HOH A 315 1555 1555 1.86 LINK MN MN A 201 O HOH A 318 1555 1555 2.29 LINK MN MN A 201 OP3B C b 5 1555 1555 2.23 LINK MN MN A 201 OP1B C b 5 1555 1555 2.38 LINK MN MN A 201 OP1C C b 5 1555 1555 2.17 LINK MN MN A 202 OP1B C b 5 1555 1555 2.47 LINK MN MN A 202 OP1C C b 5 1555 1555 2.69 LINK K C K A 203 O CHOH A 305 1555 1555 2.65 LINK K C K A 203 O HOH A 315 1555 1555 3.49 LINK K C K A 203 OP2 G b 6 1555 1555 3.20 LINK K B K A 214 O HOH A 346 1555 1555 3.43 LINK K B K A 214 O HOH B 206 1555 1555 2.80 LINK K B K A 214 OP2B C b 5 1555 1555 2.84 LINK O4 DT C 4 K A K C 101 1555 1555 3.09 LINK O6 DG C 5 K A K C 101 1555 1555 2.66 LINK K A K C 101 O HOH C 211 1555 1555 3.19 CISPEP 1 ASN A 77 PRO A 78 0 -0.58 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 305 HOH A 315 SITE 2 AC1 6 HOH A 318 C b 5 SITE 1 AC2 6 ASP A 71 GLU A 109 ASP A 132 HOH A 344 SITE 2 AC2 6 U B 4 C b 5 SITE 1 AC3 6 ASP A 192 TYR A 193 GLY A 194 HOH A 305 SITE 2 AC3 6 C b 5 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 433 HOH A 437 SITE 1 AC6 7 GLY A 76 ASN A 77 PRO A 78 HOH A 301 SITE 2 AC6 7 HOH A 317 DG C 2 DA C 3 SITE 1 AC7 8 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC7 8 GLU A 167 ASN A 170 GOL A 210 HOH A 302 SITE 1 AC8 6 HIS A 115 ARG A 118 ASN A 170 GOL A 209 SITE 2 AC8 6 HOH A 303 HOH A 387 SITE 1 AC9 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AD1 3 LYS A 89 GLU A 153 HOH A 422 SITE 1 AD2 6 PRO A 78 LEU A 149 GLU A 154 HOH A 308 SITE 2 AD2 6 HOH A 309 HOH C 209 SITE 1 AD3 5 ASP A 132 U B 4 HOH B 206 C b 5 SITE 2 AD3 5 HOH b 103 SITE 1 AD4 3 DT C 4 DG C 5 HOH C 202 CRYST1 81.199 37.746 62.051 90.00 96.25 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 0.012315 0.000000 0.001348 0.00000 SCALE2 0.000000 0.026493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016212 0.00000