HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP5 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 40 MM MG2+ AND 75 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 FRAGMENT: CATALYTIC DOMAIN RESIDUES 59-196; 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 CLEAVED 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 CLEAVED 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: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, RNA HYDROLYSIS, IN CRYSTALLO CATALYSIS, KEYWDS 2 METAL DEPENDENT CATALYSIS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 3 11-OCT-23 6DP5 1 LINK REVDAT 2 22-AUG-18 6DP5 1 JRNL REVDAT 1 15-AUG-18 6DP5 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. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 32560 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 3264 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 20.0095 - 4.0614 0.98 2680 204 0.1229 0.1343 REMARK 3 2 4.0614 - 3.2280 0.91 2568 122 0.1257 0.1463 REMARK 3 3 3.2280 - 2.8212 0.95 2689 113 0.1481 0.1658 REMARK 3 4 2.8212 - 2.5639 0.96 2690 172 0.1516 0.1762 REMARK 3 5 2.5639 - 2.3804 0.96 2661 147 0.1486 0.1835 REMARK 3 6 2.3804 - 2.2403 0.96 2685 151 0.1546 0.1900 REMARK 3 7 2.2403 - 2.1282 0.96 2713 135 0.1482 0.1891 REMARK 3 8 2.1282 - 2.0357 0.95 2658 142 0.1570 0.1804 REMARK 3 9 2.0357 - 1.9574 0.89 2484 118 0.1520 0.1744 REMARK 3 10 1.9574 - 1.8899 0.88 2501 125 0.1885 0.2198 REMARK 3 11 1.8899 - 1.8308 0.93 2589 138 0.1721 0.2126 REMARK 3 12 1.8308 - 1.7785 0.95 2683 142 0.1605 0.2024 REMARK 3 13 1.7785 - 1.7317 0.96 2629 153 0.1553 0.1792 REMARK 3 14 1.7317 - 1.6895 0.97 2734 165 0.1650 0.1879 REMARK 3 15 1.6895 - 1.6511 0.96 2690 139 0.1692 0.2452 REMARK 3 16 1.6511 - 1.6160 0.97 2724 118 0.1776 0.2227 REMARK 3 17 1.6160 - 1.5837 0.98 2726 155 0.1892 0.2212 REMARK 3 18 1.5837 - 1.5538 0.98 2668 178 0.2018 0.2273 REMARK 3 19 1.5538 - 1.5261 0.96 2761 151 0.2291 0.2849 REMARK 3 20 1.5261 - 1.5002 0.96 2653 131 0.2527 0.2514 REMARK 3 21 1.5002 - 1.4760 0.93 2684 117 0.2707 0.2366 REMARK 3 22 1.4760 - 1.4533 0.84 2273 129 0.2954 0.3334 REMARK 3 23 1.4533 - 1.4319 0.76 2180 119 0.3185 0.3714 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.26 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 : 0.009 1490 REMARK 3 ANGLE : 1.198 2045 REMARK 3 CHIRALITY : 0.083 226 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 22.415 587 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.8618 -4.4118 19.0103 REMARK 3 T TENSOR REMARK 3 T11: 0.1892 T22: 0.4906 REMARK 3 T33: 0.2975 T12: 0.0476 REMARK 3 T13: 0.0390 T23: 0.0369 REMARK 3 L TENSOR REMARK 3 L11: 9.2441 L22: 8.7712 REMARK 3 L33: 2.7144 L12: 0.4548 REMARK 3 L13: -1.7969 L23: -1.5988 REMARK 3 S TENSOR REMARK 3 S11: -0.2125 S12: 0.1868 S13: 0.1566 REMARK 3 S21: -0.4074 S22: -0.3743 S23: -0.9673 REMARK 3 S31: 0.1001 S32: 1.5738 S33: 0.4852 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.5537 -6.3365 16.3162 REMARK 3 T TENSOR REMARK 3 T11: 0.2106 T22: 0.1982 REMARK 3 T33: 0.1548 T12: 0.0148 REMARK 3 T13: 0.0065 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 7.7987 L22: 2.8156 REMARK 3 L33: 5.1648 L12: -1.5085 REMARK 3 L13: 5.3952 L23: -0.5725 REMARK 3 S TENSOR REMARK 3 S11: 0.3242 S12: 0.1308 S13: -0.2202 REMARK 3 S21: -0.2474 S22: -0.1750 S23: 0.1576 REMARK 3 S31: 0.3478 S32: -0.0728 S33: -0.1429 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4246 -1.7831 21.6044 REMARK 3 T TENSOR REMARK 3 T11: 0.1465 T22: 0.1197 REMARK 3 T33: 0.1172 T12: 0.0162 REMARK 3 T13: 0.0277 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 4.0394 L22: 1.2518 REMARK 3 L33: 3.6654 L12: -0.4010 REMARK 3 L13: 1.7332 L23: -0.4446 REMARK 3 S TENSOR REMARK 3 S11: 0.0827 S12: -0.0870 S13: -0.1562 REMARK 3 S21: -0.0671 S22: -0.0541 S23: -0.0104 REMARK 3 S31: 0.0300 S32: -0.0500 S33: -0.0295 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8542 7.9140 15.9400 REMARK 3 T TENSOR REMARK 3 T11: 0.2308 T22: 0.2301 REMARK 3 T33: 0.1963 T12: 0.1279 REMARK 3 T13: 0.0199 T23: -0.0728 REMARK 3 L TENSOR REMARK 3 L11: 4.8083 L22: 1.5738 REMARK 3 L33: 7.0919 L12: -1.9614 REMARK 3 L13: 3.4103 L23: -2.1235 REMARK 3 S TENSOR REMARK 3 S11: -0.1019 S12: 0.1170 S13: 0.5423 REMARK 3 S21: -0.2284 S22: -0.0287 S23: 0.4561 REMARK 3 S31: -0.3232 S32: -0.4855 S33: 0.0892 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5833 5.8486 24.8787 REMARK 3 T TENSOR REMARK 3 T11: 0.1855 T22: 0.1974 REMARK 3 T33: 0.1634 T12: 0.0461 REMARK 3 T13: 0.0188 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 5.6551 L22: 5.8655 REMARK 3 L33: 9.5941 L12: 4.8439 REMARK 3 L13: 7.2808 L23: 5.6711 REMARK 3 S TENSOR REMARK 3 S11: 0.1137 S12: -0.4005 S13: 0.1884 REMARK 3 S21: 0.0483 S22: -0.2720 S23: 0.1534 REMARK 3 S31: -0.1910 S32: -0.5208 S33: 0.1525 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9293 -1.0243 17.7961 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1452 REMARK 3 T33: 0.0946 T12: 0.0537 REMARK 3 T13: -0.0151 T23: 0.0471 REMARK 3 L TENSOR REMARK 3 L11: 3.9380 L22: 3.6814 REMARK 3 L33: 5.9458 L12: -1.1841 REMARK 3 L13: -1.7415 L23: 2.4038 REMARK 3 S TENSOR REMARK 3 S11: 0.1163 S12: 0.3006 S13: -0.1026 REMARK 3 S21: -0.3573 S22: -0.0109 S23: -0.1795 REMARK 3 S31: -0.0277 S32: 0.3213 S33: -0.1435 REMARK 3 TLS GROUP : 7 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): 23.8462 0.6866 5.0039 REMARK 3 T TENSOR REMARK 3 T11: 0.2795 T22: 0.2665 REMARK 3 T33: 0.1490 T12: 0.0735 REMARK 3 T13: 0.0594 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 2.6420 L22: 8.4221 REMARK 3 L33: 2.7078 L12: 0.1616 REMARK 3 L13: 2.2696 L23: -2.0186 REMARK 3 S TENSOR REMARK 3 S11: 0.0870 S12: 0.4409 S13: -0.0647 REMARK 3 S21: -0.6746 S22: -0.3018 S23: -0.2593 REMARK 3 S31: 0.1301 S32: 0.2143 S33: 0.2170 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5173 3.5684 3.2054 REMARK 3 T TENSOR REMARK 3 T11: 0.3645 T22: 0.2202 REMARK 3 T33: 0.1293 T12: 0.0623 REMARK 3 T13: -0.0263 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 3.5460 L22: 4.7248 REMARK 3 L33: 8.8641 L12: -0.9714 REMARK 3 L13: -2.4346 L23: 3.9505 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: 0.2376 S13: -0.1040 REMARK 3 S21: -0.9590 S22: -0.3379 S23: 0.1969 REMARK 3 S31: -0.4080 S32: -0.3194 S33: 0.3648 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 6DP5 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_1000235016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 20.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.4 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 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 40.94950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.75250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.94950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.75250 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: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 384 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 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: 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 -0.138 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. = 7.9 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 421 DISTANCE = 6.27 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 104.1 REMARK 620 3 HOH A 301 O 173.4 73.6 REMARK 620 4 HOH A 308 O 90.0 89.5 83.8 REMARK 620 5 HOH A 331 O 88.9 90.6 97.3 179.0 REMARK 620 6 C b 5 OP3 161.8 94.1 21.2 89.5 91.5 REMARK 620 7 C b 5 OP1 93.3 162.1 89.5 94.8 85.3 68.6 REMARK 620 8 C b 5 OP1 95.5 157.3 88.1 101.9 78.3 66.9 7.4 REMARK 620 N 1 2 3 4 5 6 7 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 99.5 REMARK 620 3 ASP A 132 OD1 135.1 94.6 REMARK 620 4 ASP A 132 OD2 104.9 148.3 53.7 REMARK 620 5 U B 4 O3' 143.3 85.6 79.8 86.8 REMARK 620 6 C b 5 OP1 87.0 106.6 129.0 94.8 57.0 REMARK 620 7 C b 5 OP1 89.0 114.8 122.8 85.9 56.8 8.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 204 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 GLU A 188 OE2 92.9 REMARK 620 3 HOH A 331 O 48.6 51.5 REMARK 620 4 HOH A 362 O 51.9 63.9 60.5 REMARK 620 5 HOH B 105 O 133.7 118.3 167.7 110.2 REMARK 620 6 C b 5 OP2 83.3 107.9 77.3 131.7 114.4 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 ASP A 192 OD2 40.8 REMARK 620 3 HOH A 301 O 50.4 81.4 REMARK 620 4 HOH A 308 O 52.4 92.0 50.2 REMARK 620 5 HOH A 330 O 85.9 54.3 91.6 134.8 REMARK 620 6 G b 6 OP2 97.4 138.1 62.2 49.2 139.9 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 LYS A 196 O REMARK 620 2 HOH B 108 O 79.0 REMARK 620 3 DG C 5 O6 67.8 11.9 REMARK 620 4 HOH C 206 O 72.7 15.6 11.1 REMARK 620 5 HOH C 207 O 77.1 8.8 10.3 7.2 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 K A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 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 EDO 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 6DP5 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP5 B 1 4 PDB 6DP5 6DP5 1 4 DBREF 6DP5 b 5 6 PDB 6DP5 6DP5 5 6 DBREF 6DP5 C 1 6 PDB 6DP5 6DP5 1 6 SEQADV 6DP5 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP5 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP5 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP5 MET A 58 UNP Q9KEI9 EXPRESSION TAG 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 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 MG A 201 1 HET MG A 202 1 HET K A 203 1 HET K 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 EDO A 212 4 HET EDO A 213 4 HET EDO A 214 4 HET K C 101 1 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 3(K 1+) FORMUL 9 IOD 4(I 1-) FORMUL 13 GOL 2(C3 H8 O3) FORMUL 15 EDO 4(C2 H6 O2) FORMUL 20 HOH *147(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'C U B 4 P C C b 5 1555 1555 1.57 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.01 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.03 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.14 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.20 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.57 LINK OD2 ASP A 132 K B K A 204 1555 1555 3.48 LINK OE2 GLU A 188 K B K A 204 1555 1555 3.14 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.98 LINK OD1 ASP A 192 K C K A 203 1555 1555 2.85 LINK OD2 ASP A 192 K C K A 203 1555 1555 3.29 LINK O LYS A 196 K K C 101 1555 4545 3.49 LINK MG MG A 201 O CHOH A 301 1555 1555 2.02 LINK MG MG A 201 O HOH A 308 1555 1555 2.06 LINK MG MG A 201 O HOH A 331 1555 1555 2.18 LINK MG MG A 201 OP3B C b 5 1555 1555 2.01 LINK MG MG A 201 OP1B C b 5 1555 1555 2.40 LINK MG MG A 201 OP1C C b 5 1555 1555 2.25 LINK MG MG A 202 O3'C U B 4 1555 1555 2.71 LINK MG MG A 202 OP1B C b 5 1555 1555 2.11 LINK MG MG A 202 OP1C C b 5 1555 1555 2.17 LINK K C K A 203 O CHOH A 301 1555 1555 2.79 LINK K C K A 203 O HOH A 308 1555 1555 3.47 LINK K C K A 203 O HOH A 330 1555 1555 3.04 LINK K C K A 203 OP2 G b 6 1555 1555 3.01 LINK K B K A 204 O HOH A 331 1555 1555 3.05 LINK K B K A 204 O HOH A 362 1555 1555 3.25 LINK K B K A 204 O HOH B 105 1555 1555 2.91 LINK K B K A 204 OP2B C b 5 1555 1555 2.56 LINK O HOH B 108 K K C 101 1555 1555 3.09 LINK O6 DG C 5 K K C 101 1555 1555 2.76 LINK K K C 101 O HOH C 206 1555 1555 3.13 LINK K K C 101 O BHOH C 207 1555 1555 2.69 CISPEP 1 ASN A 77 PRO A 78 0 -1.93 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 301 HOH A 308 SITE 2 AC1 6 HOH A 331 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 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 8 HOH A 301 HOH A 330 C b 5 G b 6 SITE 1 AC4 7 ASP A 132 GLU A 188 HOH A 303 HOH A 331 SITE 2 AC4 7 U B 4 HOH B 105 C b 5 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 3 ILE A 64 HOH A 398 HOH A 421 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 315 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 5 VAL A 150 ASN A 152 GLU A 154 HOH A 353 SITE 2 AC8 5 HOH C 202 SITE 1 AC9 4 GLU A 66 TYR A 119 SER A 125 LYS A 127 SITE 1 AD1 6 HIS A 115 GLU A 122 ARG A 123 GLU A 167 SITE 2 AD1 6 HOH A 335 HOH A 388 SITE 1 AD2 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AD3 6 ARG A 97 LEU A 157 LEU A 161 THR A 173 SITE 2 AD3 6 HOH A 306 HOH A 349 SITE 1 AD4 4 LYS A 196 HOH B 108 DG C 5 HOH C 207 CRYST1 81.899 37.505 62.254 90.00 96.48 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 0.012210 0.000000 0.001388 0.00000 SCALE2 0.000000 0.026663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016167 0.00000