HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOY TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2 MM MG2+ AND 200 MM LI+ FOR 120 TITLE 3 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 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*CP*AP*UP*CP*G)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 14 CHAIN: C; COMPND 15 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 3 11-OCT-23 6DOY 1 LINK REVDAT 2 22-AUG-18 6DOY 1 JRNL REVDAT 1 15-AUG-18 6DOY 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 31904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1601 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 19.2726 - 3.2185 0.97 2897 153 0.1213 0.1554 REMARK 3 2 3.2185 - 2.5565 0.98 2869 145 0.1391 0.1844 REMARK 3 3 2.5565 - 2.2339 0.97 2816 135 0.1469 0.1908 REMARK 3 4 2.2339 - 2.0299 0.97 2797 146 0.1459 0.1742 REMARK 3 5 2.0299 - 1.8845 0.97 2753 148 0.1642 0.2249 REMARK 3 6 1.8845 - 1.7735 0.96 2757 141 0.1671 0.2034 REMARK 3 7 1.7735 - 1.6847 0.96 2719 163 0.1760 0.2217 REMARK 3 8 1.6847 - 1.6114 0.95 2689 160 0.1921 0.2135 REMARK 3 9 1.6114 - 1.5494 0.95 2713 131 0.2191 0.2576 REMARK 3 10 1.5494 - 1.4960 0.94 2685 148 0.2718 0.3278 REMARK 3 11 1.4960 - 1.4492 0.91 2608 131 0.3074 0.2980 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1469 REMARK 3 ANGLE : 0.974 2025 REMARK 3 CHIRALITY : 0.073 220 REMARK 3 PLANARITY : 0.006 213 REMARK 3 DIHEDRAL : 23.747 576 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 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7425 -4.2211 18.8332 REMARK 3 T TENSOR REMARK 3 T11: 0.2310 T22: 0.6126 REMARK 3 T33: 0.3606 T12: 0.1045 REMARK 3 T13: 0.0398 T23: 0.0323 REMARK 3 L TENSOR REMARK 3 L11: 4.1441 L22: 7.1615 REMARK 3 L33: 8.3175 L12: -0.2945 REMARK 3 L13: -3.4981 L23: -0.7966 REMARK 3 S TENSOR REMARK 3 S11: 0.3768 S12: 0.4312 S13: 0.0248 REMARK 3 S21: -0.1698 S22: -0.4003 S23: -0.6709 REMARK 3 S31: -0.0201 S32: 1.8666 S33: 0.2689 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3167 -6.3035 16.3187 REMARK 3 T TENSOR REMARK 3 T11: 0.2204 T22: 0.1775 REMARK 3 T33: 0.2151 T12: -0.0004 REMARK 3 T13: -0.0045 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 3.3314 L22: 1.6214 REMARK 3 L33: 8.7225 L12: -0.9443 REMARK 3 L13: 5.2446 L23: -1.2254 REMARK 3 S TENSOR REMARK 3 S11: 0.3380 S12: 0.0289 S13: -0.4090 REMARK 3 S21: -0.1805 S22: -0.1080 S23: 0.1195 REMARK 3 S31: 0.4764 S32: -0.1941 S33: -0.2647 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1776 -11.6714 23.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.2696 T22: 0.2543 REMARK 3 T33: 0.3561 T12: 0.0204 REMARK 3 T13: -0.0151 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 4.7552 L22: 2.4094 REMARK 3 L33: 3.7129 L12: -0.3563 REMARK 3 L13: -4.1728 L23: -0.0103 REMARK 3 S TENSOR REMARK 3 S11: 0.1239 S12: -0.3609 S13: -0.9063 REMARK 3 S21: -0.0494 S22: 0.0342 S23: -0.4929 REMARK 3 S31: 0.6059 S32: 0.2836 S33: -0.0604 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2685 -4.9875 18.4929 REMARK 3 T TENSOR REMARK 3 T11: 0.2141 T22: 0.3295 REMARK 3 T33: 0.2323 T12: -0.0491 REMARK 3 T13: -0.0211 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 6.1607 L22: 3.1417 REMARK 3 L33: 9.5571 L12: -1.4283 REMARK 3 L13: 2.3226 L23: -5.4306 REMARK 3 S TENSOR REMARK 3 S11: 0.1805 S12: -0.6321 S13: -0.4448 REMARK 3 S21: 0.1348 S22: 0.2881 S23: 0.5471 REMARK 3 S31: 0.0739 S32: -1.1692 S33: -0.4291 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5429 2.2314 22.5964 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.1314 REMARK 3 T33: 0.1742 T12: 0.0026 REMARK 3 T13: 0.0256 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 4.5909 L22: 1.5906 REMARK 3 L33: 5.8300 L12: -1.3495 REMARK 3 L13: 3.0626 L23: -0.3744 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: -0.1298 S13: 0.1038 REMARK 3 S21: -0.0461 S22: -0.0661 S23: -0.0371 REMARK 3 S31: -0.1535 S32: -0.0920 S33: 0.0340 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6138 7.7984 16.0032 REMARK 3 T TENSOR REMARK 3 T11: 0.3558 T22: 0.4725 REMARK 3 T33: 0.3181 T12: 0.2285 REMARK 3 T13: -0.0222 T23: -0.1248 REMARK 3 L TENSOR REMARK 3 L11: 2.3543 L22: 2.1970 REMARK 3 L33: 4.7913 L12: -1.0489 REMARK 3 L13: 1.9276 L23: -1.5124 REMARK 3 S TENSOR REMARK 3 S11: 0.2233 S12: -0.1371 S13: 0.5058 REMARK 3 S21: -0.1136 S22: -0.4008 S23: 0.5666 REMARK 3 S31: -0.6002 S32: -0.9454 S33: 0.1534 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 171 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0599 6.4493 25.5796 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.3076 REMARK 3 T33: 0.2237 T12: 0.0988 REMARK 3 T13: 0.0319 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 8.7730 L22: 1.7910 REMARK 3 L33: 8.6134 L12: 1.4736 REMARK 3 L13: 6.8517 L23: 2.3612 REMARK 3 S TENSOR REMARK 3 S11: 0.1178 S12: -0.3594 S13: 0.0245 REMARK 3 S21: -0.0531 S22: -0.2572 S23: 0.0443 REMARK 3 S31: -0.3427 S32: -0.7640 S33: 0.2138 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.0047 2.7906 20.1345 REMARK 3 T TENSOR REMARK 3 T11: 0.1322 T22: 0.1983 REMARK 3 T33: 0.1848 T12: 0.0119 REMARK 3 T13: 0.0206 T23: 0.0421 REMARK 3 L TENSOR REMARK 3 L11: 4.7602 L22: 6.1011 REMARK 3 L33: 6.4105 L12: -2.3887 REMARK 3 L13: -1.1569 L23: 3.9261 REMARK 3 S TENSOR REMARK 3 S11: 0.1540 S12: 0.1431 S13: 0.3123 REMARK 3 S21: -0.2166 S22: -0.0388 S23: -0.4094 REMARK 3 S31: -0.0624 S32: 0.3655 S33: -0.2325 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4888 -9.6713 12.2787 REMARK 3 T TENSOR REMARK 3 T11: 0.3551 T22: 0.2730 REMARK 3 T33: 0.2242 T12: 0.0812 REMARK 3 T13: -0.0234 T23: -0.0508 REMARK 3 L TENSOR REMARK 3 L11: 3.8386 L22: 9.7791 REMARK 3 L33: 7.1643 L12: 5.3013 REMARK 3 L13: -1.8524 L23: 1.3957 REMARK 3 S TENSOR REMARK 3 S11: -0.2021 S12: 0.4218 S13: -0.3265 REMARK 3 S21: -0.6622 S22: 0.0084 S23: 0.1024 REMARK 3 S31: 0.8529 S32: -0.1075 S33: 0.1140 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8209 1.1748 4.5386 REMARK 3 T TENSOR REMARK 3 T11: 0.3027 T22: 0.2733 REMARK 3 T33: 0.1524 T12: 0.0678 REMARK 3 T13: 0.0351 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 5.5339 L22: 8.7047 REMARK 3 L33: 3.0488 L12: 1.4986 REMARK 3 L13: 2.6667 L23: -0.1548 REMARK 3 S TENSOR REMARK 3 S11: -0.1422 S12: 0.5361 S13: 0.2087 REMARK 3 S21: -0.7672 S22: -0.0017 S23: -0.1983 REMARK 3 S31: 0.0425 S32: 0.2656 S33: 0.1691 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4505 3.6854 3.1300 REMARK 3 T TENSOR REMARK 3 T11: 0.3574 T22: 0.2360 REMARK 3 T33: 0.1635 T12: 0.0927 REMARK 3 T13: -0.0153 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 4.5998 L22: 5.0167 REMARK 3 L33: 5.7762 L12: -0.3728 REMARK 3 L13: 0.0449 L23: 1.8015 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: 0.3267 S13: -0.1277 REMARK 3 S21: -0.8763 S22: -0.3100 S23: 0.1226 REMARK 3 S31: -0.3824 S32: -0.2641 S33: 0.3293 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234999. 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 : 31921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 19.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 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: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 40.94900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.94900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.67500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 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 205 O2 EDO C 101 1.26 REMARK 500 O1 EDO A 210 O HOH A 301 1.98 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 412 O HOH A 412 2656 1.87 REMARK 500 O HOH A 403 O HOH A 403 2656 1.89 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' -0.039 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 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 450 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 7.44 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 LI A 213 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 ASP A 132 OD1 102.2 REMARK 620 3 ASP A 132 OD2 115.5 54.8 REMARK 620 4 C B 5 OP1 113.1 144.6 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 214 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 111.3 REMARK 620 3 HOH A 337 O 98.6 95.2 REMARK 620 4 C B 5 OP1 105.4 127.5 115.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 LI A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LI A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 DBREF 6DOY A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOY B 1 6 PDB 6DOY 6DOY 1 6 DBREF 6DOY C 1 6 PDB 6DOY 6DOY 1 6 SEQADV 6DOY GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOY SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOY HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOY 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 6 A C A U C G SEQRES 1 C 6 DC DG DA DT DG DT HET IOD A 201 1 HET IOD A 202 1 HET IOD A 203 1 HET IOD A 204 1 HET GOL A 205 6 HET GOL A 206 6 HET EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET EDO A 212 4 HET LI A 213 1 HET LI A 214 1 HET EDO B 101 4 HET EDO C 101 4 HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM LI LITHIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 IOD 4(I 1-) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 EDO 8(C2 H6 O2) FORMUL 16 LI 2(LI 1+) FORMUL 20 HOH *188(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 OD1 ASP A 71 LI LI A 213 1555 1555 1.89 LINK OD2 ASP A 71 LI LI A 214 1555 1555 2.02 LINK OD1 ASP A 132 LI LI A 213 1555 1555 2.53 LINK OD2 ASP A 132 LI LI A 213 1555 1555 2.25 LINK OD1 ASP A 192 LI LI A 214 1555 1555 1.92 LINK LI LI A 213 OP1 C B 5 1555 1555 2.14 LINK LI LI A 214 O HOH A 337 1555 1555 2.06 LINK LI LI A 214 OP1 C B 5 1555 1555 1.76 CISPEP 1 ASN A 77 PRO A 78 0 1.85 SITE 1 AC1 1 TYR A 83 SITE 1 AC2 3 ILE A 64 HOH A 448 HOH A 453 SITE 1 AC3 6 ASN A 77 PRO A 78 HOH A 307 DG C 2 SITE 2 AC3 6 DA C 3 EDO C 101 SITE 1 AC4 7 GLU A 66 LEU A 94 TYR A 119 SER A 125 SITE 2 AC4 7 LYS A 127 HOH A 319 HOH A 373 SITE 1 AC5 4 LYS A 143 THR A 173 TYR A 174 HOH A 310 SITE 1 AC6 3 LYS A 89 ALA A 156 HOH A 428 SITE 1 AC7 7 PHE A 95 GLU A 96 GLU A 167 TRP A 168 SITE 2 AC7 7 THR A 171 HIS A 172 HOH A 339 SITE 1 AC8 4 THR A 148 HOH A 301 HOH A 380 DG C 5 SITE 1 AC9 6 LYS A 138 LYS A 146 HOH A 397 DC C 1 SITE 2 AC9 6 DT C 6 HOH C 206 SITE 1 AD1 7 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AD1 7 ASN A 170 HOH A 329 HOH A 386 SITE 1 AD2 6 ASP A 71 GLU A 109 ASP A 132 LI A 214 SITE 2 AD2 6 U B 4 C B 5 SITE 1 AD3 5 ASP A 71 ASP A 192 LI A 213 HOH A 337 SITE 2 AD3 5 C B 5 SITE 1 AD4 3 A B 1 HOH B 209 HOH C 205 SITE 1 AD5 2 GOL A 205 HOH C 202 CRYST1 81.898 37.350 62.034 90.00 96.81 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 0.001459 0.00000 SCALE2 0.000000 0.026774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016235 0.00000