HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOJ TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2 MM MG2+ AND 5 MM K+ FOR 120 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 61-196); COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF INTACT RNA (5'- COMPND 10 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF INTACT RNA (5'- COMPND 15 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 16 CHAIN: b; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 20 CHAIN: C; COMPND 21 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_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 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 6DOJ 1 LINK REVDAT 1 15-AUG-18 6DOJ 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 36463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1797 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 20.0202 - 3.2943 0.99 2782 135 0.1201 0.1610 REMARK 3 2 3.2943 - 2.6166 1.00 2725 143 0.1378 0.1801 REMARK 3 3 2.6166 - 2.2864 1.00 2730 128 0.1421 0.1870 REMARK 3 4 2.2864 - 2.0776 1.00 2691 131 0.1381 0.1850 REMARK 3 5 2.0776 - 1.9288 1.00 2696 146 0.1446 0.1633 REMARK 3 6 1.9288 - 1.8152 1.00 2665 150 0.1577 0.2267 REMARK 3 7 1.8152 - 1.7243 1.00 2673 148 0.1625 0.1874 REMARK 3 8 1.7243 - 1.6493 1.00 2666 160 0.1680 0.1935 REMARK 3 9 1.6493 - 1.5858 1.00 2704 131 0.1863 0.2571 REMARK 3 10 1.5858 - 1.5311 1.00 2683 140 0.2023 0.2004 REMARK 3 11 1.5311 - 1.4833 1.00 2635 129 0.2288 0.2388 REMARK 3 12 1.4833 - 1.4409 0.99 2629 162 0.2662 0.2891 REMARK 3 13 1.4409 - 1.4030 0.88 2387 94 0.3248 0.3513 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.59 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 1462 REMARK 3 ANGLE : 1.067 2018 REMARK 3 CHIRALITY : 0.072 219 REMARK 3 PLANARITY : 0.006 211 REMARK 3 DIHEDRAL : 24.556 572 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7827 -4.2794 18.9327 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.5217 REMARK 3 T33: 0.2844 T12: 0.0778 REMARK 3 T13: 0.0238 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 4.9488 L22: 9.4141 REMARK 3 L33: 7.6280 L12: 0.9268 REMARK 3 L13: -4.9849 L23: -1.7442 REMARK 3 S TENSOR REMARK 3 S11: 0.1509 S12: 0.4749 S13: 0.0630 REMARK 3 S21: -0.3157 S22: -0.3675 S23: -0.6769 REMARK 3 S31: 0.2812 S32: 1.8543 S33: 0.2887 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3470 -6.2970 16.4517 REMARK 3 T TENSOR REMARK 3 T11: 0.2162 T22: 0.1413 REMARK 3 T33: 0.2257 T12: 0.0014 REMARK 3 T13: -0.0231 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 8.6665 L22: 1.0066 REMARK 3 L33: 5.2841 L12: -1.2036 REMARK 3 L13: 4.9457 L23: -1.0204 REMARK 3 S TENSOR REMARK 3 S11: 0.4249 S12: 0.0096 S13: -0.5460 REMARK 3 S21: -0.2008 S22: -0.0981 S23: 0.0984 REMARK 3 S31: 0.4201 S32: -0.1609 S33: -0.3672 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9347 -11.5804 24.0347 REMARK 3 T TENSOR REMARK 3 T11: 0.2860 T22: 0.2281 REMARK 3 T33: 0.3732 T12: 0.0280 REMARK 3 T13: -0.0488 T23: 0.0583 REMARK 3 L TENSOR REMARK 3 L11: 6.2430 L22: 7.1118 REMARK 3 L33: 5.0414 L12: -0.4928 REMARK 3 L13: -5.2860 L23: -0.0839 REMARK 3 S TENSOR REMARK 3 S11: -0.0371 S12: -0.6117 S13: -1.5081 REMARK 3 S21: 0.0616 S22: -0.0217 S23: -0.5353 REMARK 3 S31: 0.8148 S32: 0.3722 S33: 0.0755 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9780 -0.9575 23.3538 REMARK 3 T TENSOR REMARK 3 T11: 0.1291 T22: 0.1255 REMARK 3 T33: 0.1507 T12: 0.0106 REMARK 3 T13: 0.0215 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 5.0879 L22: 0.8261 REMARK 3 L33: 4.4397 L12: -0.3329 REMARK 3 L13: 3.1666 L23: -0.0048 REMARK 3 S TENSOR REMARK 3 S11: 0.0683 S12: -0.4121 S13: -0.0702 REMARK 3 S21: -0.0236 S22: -0.0489 S23: 0.0533 REMARK 3 S31: 0.0603 S32: -0.3952 S33: -0.0121 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0397 9.3647 16.6190 REMARK 3 T TENSOR REMARK 3 T11: 0.3182 T22: 0.1269 REMARK 3 T33: 0.2356 T12: -0.0057 REMARK 3 T13: 0.0135 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 8.1743 L22: 4.3405 REMARK 3 L33: 8.3184 L12: -5.6219 REMARK 3 L13: -0.6836 L23: 1.7963 REMARK 3 S TENSOR REMARK 3 S11: 0.2456 S12: 0.1315 S13: 0.5475 REMARK 3 S21: -0.0986 S22: -0.1668 S23: -0.5956 REMARK 3 S31: -1.0664 S32: 0.2345 S33: -0.0565 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7569 7.7251 16.2029 REMARK 3 T TENSOR REMARK 3 T11: 0.2951 T22: 0.3561 REMARK 3 T33: 0.2321 T12: 0.2250 REMARK 3 T13: -0.0015 T23: -0.0919 REMARK 3 L TENSOR REMARK 3 L11: 7.2977 L22: 6.1090 REMARK 3 L33: 8.5079 L12: 1.6637 REMARK 3 L13: 3.9706 L23: 1.2196 REMARK 3 S TENSOR REMARK 3 S11: 0.2732 S12: -0.1434 S13: 0.3871 REMARK 3 S21: 0.0705 S22: -0.3681 S23: 0.5495 REMARK 3 S31: -0.3868 S32: -1.0623 S33: 0.1072 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4893 5.7843 24.9192 REMARK 3 T TENSOR REMARK 3 T11: 0.2297 T22: 0.3276 REMARK 3 T33: 0.2227 T12: 0.0907 REMARK 3 T13: 0.0063 T23: -0.0456 REMARK 3 L TENSOR REMARK 3 L11: 7.3032 L22: 2.1775 REMARK 3 L33: 4.5277 L12: 2.0827 REMARK 3 L13: 5.6670 L23: 1.8678 REMARK 3 S TENSOR REMARK 3 S11: 0.1394 S12: -0.4414 S13: 0.0276 REMARK 3 S21: 0.0273 S22: -0.2248 S23: 0.0499 REMARK 3 S31: -0.2999 S32: -0.7738 S33: 0.1254 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0314 8.3524 30.5332 REMARK 3 T TENSOR REMARK 3 T11: 0.2198 T22: 0.2080 REMARK 3 T33: 0.2277 T12: 0.0082 REMARK 3 T13: -0.0118 T23: -0.0295 REMARK 3 L TENSOR REMARK 3 L11: 4.9767 L22: 8.1420 REMARK 3 L33: 9.5112 L12: -5.8602 REMARK 3 L13: -6.5933 L23: 6.8145 REMARK 3 S TENSOR REMARK 3 S11: 0.1471 S12: -0.6813 S13: 0.7140 REMARK 3 S21: -0.1236 S22: 0.2991 S23: -0.4865 REMARK 3 S31: -0.4730 S32: 0.3951 S33: -0.2404 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.6311 -0.9638 12.3408 REMARK 3 T TENSOR REMARK 3 T11: 0.2510 T22: 0.3579 REMARK 3 T33: 0.2359 T12: 0.0834 REMARK 3 T13: 0.0764 T23: 0.0404 REMARK 3 L TENSOR REMARK 3 L11: 3.1897 L22: 4.3656 REMARK 3 L33: 4.8519 L12: 0.0537 REMARK 3 L13: 0.7401 L23: 4.3831 REMARK 3 S TENSOR REMARK 3 S11: 0.3579 S12: 0.7907 S13: -0.0595 REMARK 3 S21: -0.4637 S22: -0.1946 S23: -0.6262 REMARK 3 S31: -0.0289 S32: 0.4737 S33: -0.2526 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5009 -9.4580 12.5204 REMARK 3 T TENSOR REMARK 3 T11: 0.3698 T22: 0.2449 REMARK 3 T33: 0.2916 T12: 0.0790 REMARK 3 T13: -0.0420 T23: -0.0656 REMARK 3 L TENSOR REMARK 3 L11: 5.7336 L22: 4.9216 REMARK 3 L33: 4.9218 L12: 2.4347 REMARK 3 L13: -5.1886 L23: -1.3358 REMARK 3 S TENSOR REMARK 3 S11: 0.0954 S12: 0.7400 S13: -0.5465 REMARK 3 S21: -0.4663 S22: 0.0327 S23: 0.2427 REMARK 3 S31: 0.6990 S32: -0.1422 S33: -0.0639 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN 'B' AND (RESID 1 THROUGH 4)) OR (CHAIN 'B' REMARK 3 AND (RESID 5 THROUGH 6)) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8593 1.2159 4.5603 REMARK 3 T TENSOR REMARK 3 T11: 0.3250 T22: 0.2729 REMARK 3 T33: 0.1788 T12: 0.0953 REMARK 3 T13: 0.0535 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 3.9124 L22: 8.8269 REMARK 3 L33: 4.5802 L12: -0.7568 REMARK 3 L13: 2.8389 L23: -2.2330 REMARK 3 S TENSOR REMARK 3 S11: 0.0989 S12: 0.5275 S13: -0.0976 REMARK 3 S21: -0.8241 S22: -0.3959 S23: -0.3539 REMARK 3 S31: 0.1718 S32: 0.3748 S33: 0.2782 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5016 3.6705 3.2427 REMARK 3 T TENSOR REMARK 3 T11: 0.3847 T22: 0.2165 REMARK 3 T33: 0.1642 T12: 0.0906 REMARK 3 T13: -0.0281 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 4.6624 L22: 5.6744 REMARK 3 L33: 4.6264 L12: -0.7967 REMARK 3 L13: -1.1825 L23: 3.4588 REMARK 3 S TENSOR REMARK 3 S11: 0.0513 S12: 0.3423 S13: -0.2205 REMARK 3 S21: -1.0535 S22: -0.3723 S23: 0.1527 REMARK 3 S31: -0.6632 S32: -0.3160 S33: 0.3402 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 6DOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-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 : DOUBLE CRYSTAL SI(220) 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 : 36467 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 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: PDB ENTRY 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM REMARK 280 POTASSIUM IODIDE, 5 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 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 40.93650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.68050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.93650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.68050 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: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 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 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 OE1 GLU A 154 O2 EDO A 210 2.00 REMARK 500 OG1 THR A 90 O HOH A 301 2.12 REMARK 500 O HOH A 317 O HOH A 445 2.13 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 A 424 O HOH A 424 2656 1.82 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 466 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 467 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 468 DISTANCE = 7.42 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 97.6 REMARK 620 3 HOH A 323 O 88.9 91.7 REMARK 620 4 HOH A 329 O 88.8 93.7 174.3 REMARK 620 5 HOH A 330 O 174.6 77.7 94.0 88.8 REMARK 620 6 C b 5 OP1 97.9 163.2 82.2 93.1 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 102.8 REMARK 620 3 ASP A 132 OD1 138.4 96.7 REMARK 620 4 ASP A 132 OD2 111.0 144.0 49.2 REMARK 620 5 U B 4 O3' 134.8 81.0 84.1 83.8 REMARK 620 6 C b 5 OP1 81.2 110.6 125.2 87.0 56.3 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 HOH A 329 O 58.8 REMARK 620 3 HOH A 330 O 53.7 62.1 REMARK 620 4 HOH A 360 O 64.9 110.5 52.7 REMARK 620 5 G b 6 OP2 104.1 54.3 66.2 110.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 102 DBREF 6DOJ A 61 195 UNP Q9KEI9 RNH1_BACHD 61 195 DBREF 6DOJ B 1 4 PDB 6DOJ 6DOJ 1 4 DBREF 6DOJ b 5 6 PDB 6DOJ 6DOJ 5 6 DBREF 6DOJ C 1 6 PDB 6DOJ 6DOJ 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 MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET GOL A 205 6 HET GOL A 206 6 HET GOL A 207 6 HET EDO A 208 4 HET GOL A 209 6 HET EDO A 210 4 HET EDO A 211 4 HET EDO C 101 4 HET EDO C 102 4 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K K 1+ FORMUL 8 IOD I 1- FORMUL 9 GOL 4(C3 H8 O3) FORMUL 12 EDO 5(C2 H6 O2) FORMUL 18 HOH *203(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 1.60 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.10 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.19 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.26 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.31 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.82 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.96 LINK OD1 ASP A 192 K K A 203 1555 1555 3.00 LINK MG MG A 201 O HOH A 323 1555 1555 2.10 LINK MG MG A 201 O HOH A 329 1555 1555 2.05 LINK MG MG A 201 O HOH A 330 1555 1555 2.27 LINK MG MG A 201 OP1 C b 5 1555 1555 2.15 LINK MG MG A 202 O3' U B 4 1555 1555 2.69 LINK MG MG A 202 OP1 C b 5 1555 1555 2.51 LINK K K A 203 O HOH A 329 1555 1555 2.97 LINK K K A 203 O HOH A 330 1555 1555 2.90 LINK K K A 203 O HOH A 360 1555 1555 3.08 LINK K K A 203 OP2 G b 6 1555 1555 2.99 CISPEP 1 ASN A 77 PRO A 78 0 -0.87 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 323 HOH A 329 SITE 2 AC1 6 HOH A 330 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 8 ASP A 192 TYR A 193 GLY A 194 ARG A 195 SITE 2 AC3 8 HOH A 329 HOH A 330 HOH A 360 G b 6 SITE 1 AC4 4 ILE A 64 EDO A 211 HOH A 463 HOH A 467 SITE 1 AC5 5 GLY A 76 ASN A 77 PRO A 78 HOH B 107 SITE 2 AC5 5 DG C 2 SITE 1 AC6 9 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC6 9 GLU A 167 ASN A 170 HOH A 302 HOH A 342 SITE 3 AC6 9 HOH A 393 SITE 1 AC7 6 GLU A 66 ARG A 123 SER A 125 LYS A 127 SITE 2 AC7 6 HOH A 307 HOH A 319 SITE 1 AC8 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AC9 8 TYR A 83 LEU A 111 HIS A 115 ARG A 118 SITE 2 AC9 8 HOH A 308 HOH A 361 HOH A 393 HOH A 408 SITE 1 AD1 4 VAL A 150 ASN A 152 GLU A 154 HOH A 315 SITE 1 AD2 5 ARG A 126 GLU A 175 IOD A 204 HOH A 381 SITE 2 AD2 5 HOH A 468 SITE 1 AD3 4 DA C 3 DT C 4 EDO C 102 HOH C 204 SITE 1 AD4 6 HOH A 345 DT C 4 DG C 5 EDO C 101 SITE 2 AD4 6 HOH C 205 HOH C 210 CRYST1 81.873 37.361 62.275 90.00 96.71 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 0.012214 0.000000 0.001438 0.00000 SCALE2 0.000000 0.026766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016169 0.00000