HEADER HYDROLASE/DNA/RNA 05-JUN-18 6DMN TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: SOAKED IN 2 MM CA2+ AND 200 MM K+ 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'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3'); 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; 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: BACILLUS HALODURANS; SOURCE 14 ORGANISM_TAXID: 86665; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 18 ORGANISM_TAXID: 86665; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 22 ORGANISM_TAXID: 86665 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 2 11-OCT-23 6DMN 1 LINK REVDAT 1 15-AUG-18 6DMN 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. 1.27 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 46730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2369 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 19.8667 - 3.2611 0.80 2290 127 0.1529 0.1748 REMARK 3 2 3.2611 - 2.5903 0.97 2718 145 0.1384 0.1748 REMARK 3 3 2.5903 - 2.2634 0.97 2713 144 0.1398 0.1639 REMARK 3 4 2.2634 - 2.0566 0.98 2721 141 0.1361 0.1514 REMARK 3 5 2.0566 - 1.9094 0.97 2727 122 0.1416 0.1555 REMARK 3 6 1.9094 - 1.7969 0.97 2646 150 0.1498 0.1560 REMARK 3 7 1.7969 - 1.7069 0.96 2664 148 0.1403 0.1590 REMARK 3 8 1.7069 - 1.6327 0.96 2654 150 0.1433 0.1588 REMARK 3 9 1.6327 - 1.5698 0.95 2623 138 0.1486 0.1690 REMARK 3 10 1.5698 - 1.5157 0.95 2632 129 0.1568 0.1997 REMARK 3 11 1.5157 - 1.4683 0.94 2602 160 0.1654 0.1741 REMARK 3 12 1.4683 - 1.4264 0.94 2596 118 0.1794 0.2003 REMARK 3 13 1.4264 - 1.3888 0.94 2581 135 0.1888 0.1909 REMARK 3 14 1.3888 - 1.3549 0.94 2562 132 0.2035 0.2123 REMARK 3 15 1.3549 - 1.3241 0.93 2587 147 0.2057 0.2248 REMARK 3 16 1.3241 - 1.2960 0.93 2552 136 0.2180 0.2384 REMARK 3 17 1.2960 - 1.2700 0.91 2493 147 0.2358 0.2224 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.27 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 1461 REMARK 3 ANGLE : 0.998 2027 REMARK 3 CHIRALITY : 0.069 221 REMARK 3 PLANARITY : 0.007 210 REMARK 3 DIHEDRAL : 23.847 568 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 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.1792 -3.8784 19.0153 REMARK 3 T TENSOR REMARK 3 T11: 0.2005 T22: 0.4811 REMARK 3 T33: 0.2697 T12: 0.1124 REMARK 3 T13: 0.0299 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 4.3705 L22: 1.6154 REMARK 3 L33: 3.4519 L12: 2.5781 REMARK 3 L13: -3.8371 L23: -2.1995 REMARK 3 S TENSOR REMARK 3 S11: 0.3267 S12: 0.4005 S13: -0.0115 REMARK 3 S21: -0.1579 S22: -0.1738 S23: -0.2436 REMARK 3 S31: -0.1682 S32: 0.3308 S33: -0.2850 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.9434 -6.0650 16.5043 REMARK 3 T TENSOR REMARK 3 T11: 0.1753 T22: 0.1409 REMARK 3 T33: 0.1472 T12: 0.0086 REMARK 3 T13: 0.0013 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 9.4130 L22: 1.6879 REMARK 3 L33: 5.3229 L12: -1.5408 REMARK 3 L13: 5.2297 L23: -1.1290 REMARK 3 S TENSOR REMARK 3 S11: 0.2694 S12: 0.0718 S13: -0.4039 REMARK 3 S21: -0.1001 S22: -0.1283 S23: 0.0505 REMARK 3 S31: 0.2886 S32: 0.0207 S33: -0.1948 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2144 -11.3753 23.8093 REMARK 3 T TENSOR REMARK 3 T11: 0.2432 T22: 0.1785 REMARK 3 T33: 0.3482 T12: 0.0705 REMARK 3 T13: -0.0234 T23: 0.0705 REMARK 3 L TENSOR REMARK 3 L11: 4.6065 L22: 6.4731 REMARK 3 L33: 7.9045 L12: -4.0161 REMARK 3 L13: -4.5199 L23: 1.2637 REMARK 3 S TENSOR REMARK 3 S11: -0.0364 S12: -0.4929 S13: -1.3019 REMARK 3 S21: 0.0455 S22: -0.0485 S23: -0.5113 REMARK 3 S31: 0.9081 S32: 0.4326 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4018 -0.9796 23.6758 REMARK 3 T TENSOR REMARK 3 T11: 0.0961 T22: 0.1034 REMARK 3 T33: 0.1160 T12: 0.0103 REMARK 3 T13: 0.0120 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 3.4690 L22: 0.7425 REMARK 3 L33: 3.8444 L12: -0.2652 REMARK 3 L13: 2.0764 L23: 0.2697 REMARK 3 S TENSOR REMARK 3 S11: 0.0428 S12: -0.2859 S13: -0.0820 REMARK 3 S21: 0.0096 S22: -0.0509 S23: 0.0339 REMARK 3 S31: 0.0516 S32: -0.2401 S33: 0.0089 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.1060 9.5162 16.5888 REMARK 3 T TENSOR REMARK 3 T11: 0.2450 T22: 0.1138 REMARK 3 T33: 0.1721 T12: -0.0192 REMARK 3 T13: 0.0021 T23: 0.0381 REMARK 3 L TENSOR REMARK 3 L11: 7.7373 L22: 9.0109 REMARK 3 L33: 7.8650 L12: -6.5092 REMARK 3 L13: -1.4001 L23: 2.7663 REMARK 3 S TENSOR REMARK 3 S11: 0.0960 S12: 0.1126 S13: 0.5296 REMARK 3 S21: -0.1220 S22: -0.0511 S23: -0.5090 REMARK 3 S31: -0.7707 S32: 0.2248 S33: -0.0558 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8038 7.8157 16.0247 REMARK 3 T TENSOR REMARK 3 T11: 0.2976 T22: 0.4061 REMARK 3 T33: 0.2175 T12: 0.1812 REMARK 3 T13: -0.0097 T23: -0.0942 REMARK 3 L TENSOR REMARK 3 L11: 4.7233 L22: 2.4797 REMARK 3 L33: 3.0282 L12: 0.2532 REMARK 3 L13: 0.6376 L23: -1.4936 REMARK 3 S TENSOR REMARK 3 S11: 0.0908 S12: -0.4217 S13: 0.4066 REMARK 3 S21: -0.1567 S22: -0.3117 S23: 0.4994 REMARK 3 S31: -0.5297 S32: -1.0871 S33: 0.0301 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7219 6.0732 25.1243 REMARK 3 T TENSOR REMARK 3 T11: 0.1530 T22: 0.2586 REMARK 3 T33: 0.1540 T12: 0.0527 REMARK 3 T13: 0.0013 T23: -0.0559 REMARK 3 L TENSOR REMARK 3 L11: 3.5475 L22: 2.4264 REMARK 3 L33: 5.8101 L12: 0.8198 REMARK 3 L13: 4.0128 L23: 1.0512 REMARK 3 S TENSOR REMARK 3 S11: 0.1034 S12: -0.2984 S13: 0.0805 REMARK 3 S21: -0.0680 S22: -0.2932 S23: 0.2001 REMARK 3 S31: -0.1499 S32: -0.7638 S33: 0.2347 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.7060 8.4473 30.3183 REMARK 3 T TENSOR REMARK 3 T11: 0.1593 T22: 0.1838 REMARK 3 T33: 0.1657 T12: -0.0106 REMARK 3 T13: -0.0118 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 3.8647 L22: 8.4039 REMARK 3 L33: 8.4095 L12: -5.5743 REMARK 3 L13: -4.6662 L23: 5.8078 REMARK 3 S TENSOR REMARK 3 S11: -0.0278 S12: -0.5557 S13: 0.3772 REMARK 3 S21: 0.0172 S22: 0.2438 S23: -0.2870 REMARK 3 S31: -0.2378 S32: 0.3124 S33: -0.1058 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.8110 -0.7069 12.2223 REMARK 3 T TENSOR REMARK 3 T11: 0.2252 T22: 0.4008 REMARK 3 T33: 0.1897 T12: 0.0820 REMARK 3 T13: 0.0750 T23: 0.0398 REMARK 3 L TENSOR REMARK 3 L11: 0.7450 L22: 7.3482 REMARK 3 L33: 4.5091 L12: -0.3720 REMARK 3 L13: -0.2787 L23: 5.3976 REMARK 3 S TENSOR REMARK 3 S11: 0.1963 S12: 0.5723 S13: 0.1343 REMARK 3 S21: -0.5451 S22: -0.1591 S23: -0.6583 REMARK 3 S31: -0.0015 S32: 0.7226 S33: -0.2041 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.7882 -9.5068 12.5386 REMARK 3 T TENSOR REMARK 3 T11: 0.3665 T22: 0.2520 REMARK 3 T33: 0.2153 T12: 0.1033 REMARK 3 T13: -0.0074 T23: -0.0526 REMARK 3 L TENSOR REMARK 3 L11: 3.7413 L22: 3.5711 REMARK 3 L33: 7.4176 L12: 2.1604 REMARK 3 L13: -4.3035 L23: -0.6397 REMARK 3 S TENSOR REMARK 3 S11: -0.0970 S12: 0.5003 S13: -0.4732 REMARK 3 S21: -0.5096 S22: -0.1453 S23: -0.0679 REMARK 3 S31: 0.8416 S32: 0.0365 S33: 0.1271 REMARK 3 TLS GROUP : 11 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): 23.0193 0.3681 4.5184 REMARK 3 T TENSOR REMARK 3 T11: 0.2302 T22: 0.1790 REMARK 3 T33: 0.1093 T12: 0.0784 REMARK 3 T13: 0.0260 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 3.3452 L22: 6.5663 REMARK 3 L33: 5.8700 L12: -0.7793 REMARK 3 L13: 1.4685 L23: -0.4390 REMARK 3 S TENSOR REMARK 3 S11: 0.0846 S12: 0.2901 S13: -0.0537 REMARK 3 S21: -0.7812 S22: -0.3917 S23: -0.2096 REMARK 3 S31: 0.1765 S32: 0.4462 S33: 0.1742 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6340 3.8408 3.1441 REMARK 3 T TENSOR REMARK 3 T11: 0.2902 T22: 0.1760 REMARK 3 T33: 0.1209 T12: 0.0893 REMARK 3 T13: -0.0251 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 4.1371 L22: 4.5460 REMARK 3 L33: 9.5397 L12: -0.4736 REMARK 3 L13: -0.1875 L23: 2.7074 REMARK 3 S TENSOR REMARK 3 S11: 0.0806 S12: 0.3803 S13: -0.0408 REMARK 3 S21: -0.7566 S22: -0.3150 S23: 0.0788 REMARK 3 S31: -0.4817 S32: -0.2056 S33: 0.2654 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 6DMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234926. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-14 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-BM-B 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 : 46733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 19.864 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 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: MOLREP REMARK 200 STARTING MODEL: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 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 40.73250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.84050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.73250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.84050 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: 5060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 418 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 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 ARG A 195 CB CG CD NE CZ NH1 NH2 REMARK 470 A B 1 O2' REMARK 470 G b 6 O2' 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 417 O HOH A 417 2656 1.91 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 G b 6 O5' G b 6 C5' -0.058 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 439 DISTANCE = 6.62 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 96.5 REMARK 620 3 EDO A 211 O1 154.0 79.5 REMARK 620 4 HOH A 302 O 147.0 92.1 59.0 REMARK 620 5 HOH A 311 O 78.3 85.2 126.3 70.7 REMARK 620 6 HOH A 340 O 82.8 86.1 71.4 129.7 158.1 REMARK 620 7 C b 5 OP1 88.6 171.7 93.1 87.1 102.3 88.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA 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 GLU A 109 OE2 78.7 45.9 REMARK 620 4 ASP A 132 OD1 149.8 91.3 89.2 REMARK 620 5 ASP A 132 OD2 118.3 141.8 132.9 53.2 REMARK 620 6 HOH A 355 O 79.4 104.2 60.4 70.6 79.1 REMARK 620 7 U B 4 O3' 130.5 73.6 118.3 79.7 85.1 150.2 REMARK 620 8 C b 5 OP1 82.5 103.0 138.8 122.6 88.2 149.4 53.4 REMARK 620 N 1 2 3 4 5 6 7 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 DG C 5 O6 REMARK 620 2 HOH C 206 O 76.6 REMARK 620 3 HOH C 215 O 111.5 104.7 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 CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 DBREF 6DMN A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DMN B 1 4 PDB 6DMN 6DMN 1 4 DBREF 6DMN b 5 6 PDB 6DMN 6DMN 5 6 DBREF 6DMN C 1 6 PDB 6DMN 6DMN 1 6 SEQADV 6DMN GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMN SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMN HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMN 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 CA A 201 1 HET CA A 202 1 HET IOD A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET GOL A 207 6 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET K C 101 1 HET GOL C 102 6 HETNAM CA CALCIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 CA 2(CA 2+) FORMUL 7 IOD 4(I 1-) FORMUL 11 GOL 2(C3 H8 O3) FORMUL 12 EDO 4(C2 H6 O2) FORMUL 16 K K 1+ FORMUL 18 HOH *170(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' U B 4 P C b 5 1555 1555 1.60 LINK OD2 ASP A 71 CA CA A 201 1555 1555 2.33 LINK OD1 ASP A 71 CA CA A 202 1555 1555 2.20 LINK OE1 GLU A 109 CA CA A 202 1555 1555 2.40 LINK OE2 GLU A 109 CA CA A 202 1555 1555 3.02 LINK OD1 ASP A 132 CA CA A 202 1555 1555 2.36 LINK OD2 ASP A 132 CA CA A 202 1555 1555 2.51 LINK OD1 ASP A 192 CA CA A 201 1555 1555 2.25 LINK CA CA A 201 O1 AEDO A 211 1555 1555 2.46 LINK CA CA A 201 O AHOH A 302 1555 1555 2.38 LINK CA CA A 201 O HOH A 311 1555 1555 2.25 LINK CA CA A 201 O HOH A 340 1555 1555 2.26 LINK CA CA A 201 OP1 C b 5 1555 1555 2.37 LINK CA CA A 202 O HOH A 355 1555 1555 2.76 LINK CA CA A 202 O3' U B 4 1555 1555 2.83 LINK CA CA A 202 OP1 C b 5 1555 1555 2.56 LINK O6 DG C 5 K K C 101 1555 1555 2.69 LINK K K C 101 O HOH C 206 1555 1555 3.39 LINK K K C 101 O HOH C 215 1555 1555 2.63 CISPEP 1 ASN A 77 PRO A 78 0 2.98 SITE 1 AC1 7 ASP A 71 ASP A 192 EDO A 211 HOH A 302 SITE 2 AC1 7 HOH A 311 HOH A 340 C b 5 SITE 1 AC2 6 ASP A 71 GLU A 109 ASP A 132 HOH A 355 SITE 2 AC2 6 U B 4 C b 5 SITE 1 AC3 1 TYR A 83 SITE 1 AC4 2 ILE A 64 HOH A 411 SITE 1 AC5 1 HIS A 172 SITE 1 AC6 5 GLU A 66 LEU A 94 SER A 125 LYS A 127 SITE 2 AC6 5 HOH A 343 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 DG C 2 SITE 2 AC7 6 DA C 3 G b 6 SITE 1 AC8 9 HIS A 115 ARG A 118 TYR A 119 GLU A 122 SITE 2 AC8 9 ARG A 123 GLU A 167 ASN A 170 HOH A 356 SITE 3 AC8 9 HOH A 360 SITE 1 AC9 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AD1 7 GLU A 188 ASP A 192 GLY A 194 CA A 201 SITE 2 AD1 7 HOH A 302 HOH A 340 C b 5 SITE 1 AD2 3 DT C 4 DG C 5 HOH C 215 SITE 1 AD3 6 THR A 148 DT C 4 DG C 5 HOH C 201 SITE 2 AD3 6 HOH C 202 HOH C 209 CRYST1 81.465 37.681 62.022 90.00 95.93 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 0.012275 0.000000 0.001275 0.00000 SCALE2 0.000000 0.026539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016210 0.00000