HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP8 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 5 MM MG2+ AND 200 MM LI+ FOR 240 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*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 14 CHAIN: b; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 18 CHAIN: C; COMPND 19 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; 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, 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 3 11-OCT-23 6DP8 1 LINK REVDAT 2 22-AUG-18 6DP8 1 JRNL REVDAT 1 15-AUG-18 6DP8 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. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 81810 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 4068 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 23.4589 - 4.0576 0.99 2802 115 0.1344 0.1328 REMARK 3 2 4.0576 - 3.2233 0.99 2801 137 0.1196 0.1515 REMARK 3 3 3.2233 - 2.8166 0.99 2778 129 0.1394 0.1543 REMARK 3 4 2.8166 - 2.5595 0.99 2787 143 0.1429 0.1649 REMARK 3 5 2.5595 - 2.3762 0.98 2745 136 0.1401 0.1558 REMARK 3 6 2.3762 - 2.2362 0.98 2746 154 0.1343 0.1740 REMARK 3 7 2.2362 - 2.1243 0.98 2767 140 0.1275 0.1459 REMARK 3 8 2.1243 - 2.0319 0.98 2721 136 0.1282 0.1305 REMARK 3 9 2.0319 - 1.9537 0.97 2718 145 0.1311 0.1487 REMARK 3 10 1.9537 - 1.8863 0.97 2700 177 0.1398 0.1749 REMARK 3 11 1.8863 - 1.8274 0.97 2781 134 0.1477 0.1948 REMARK 3 12 1.8274 - 1.7751 0.97 2643 157 0.1403 0.1698 REMARK 3 13 1.7751 - 1.7284 0.96 2683 136 0.1356 0.1554 REMARK 3 14 1.7284 - 1.6863 0.96 2751 135 0.1382 0.1593 REMARK 3 15 1.6863 - 1.6479 0.96 2660 147 0.1507 0.1825 REMARK 3 16 1.6479 - 1.6129 0.96 2693 151 0.1602 0.2148 REMARK 3 17 1.6129 - 1.5806 0.96 2682 146 0.1645 0.2204 REMARK 3 18 1.5806 - 1.5508 0.96 2656 137 0.1777 0.1935 REMARK 3 19 1.5508 - 1.5231 0.95 2674 144 0.1875 0.2339 REMARK 3 20 1.5231 - 1.4973 0.95 2611 153 0.2048 0.1997 REMARK 3 21 1.4973 - 1.4731 0.95 2716 143 0.2086 0.2632 REMARK 3 22 1.4731 - 1.4505 0.94 2554 146 0.2190 0.2651 REMARK 3 23 1.4505 - 1.4292 0.95 2749 142 0.2369 0.2596 REMARK 3 24 1.4292 - 1.4090 0.95 2628 147 0.2512 0.2822 REMARK 3 25 1.4090 - 1.3900 0.94 2625 124 0.2618 0.2901 REMARK 3 26 1.3900 - 1.3719 0.94 2631 122 0.2835 0.2440 REMARK 3 27 1.3719 - 1.3548 0.93 2602 152 0.2850 0.3539 REMARK 3 28 1.3548 - 1.3385 0.91 2586 116 0.3141 0.3460 REMARK 3 29 1.3385 - 1.3229 0.80 2252 124 0.3291 0.3653 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) : 18.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1496 REMARK 3 ANGLE : 1.056 2047 REMARK 3 CHIRALITY : 0.071 221 REMARK 3 PLANARITY : 0.007 214 REMARK 3 DIHEDRAL : 25.394 587 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.1107 -3.5314 19.1328 REMARK 3 T TENSOR REMARK 3 T11: 0.1769 T22: 0.4135 REMARK 3 T33: 0.3720 T12: 0.0709 REMARK 3 T13: 0.0333 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 3.3633 L22: 8.6429 REMARK 3 L33: 3.4392 L12: 1.4583 REMARK 3 L13: -3.0019 L23: -0.6921 REMARK 3 S TENSOR REMARK 3 S11: 0.1559 S12: 0.7585 S13: 0.5098 REMARK 3 S21: -0.5628 S22: -0.1863 S23: -1.0167 REMARK 3 S31: -0.0523 S32: 1.1272 S33: 0.0213 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.0259 -6.3342 16.1651 REMARK 3 T TENSOR REMARK 3 T11: 0.1331 T22: 0.1083 REMARK 3 T33: 0.1514 T12: -0.0036 REMARK 3 T13: 0.0030 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 4.4704 L22: 0.9431 REMARK 3 L33: 7.6238 L12: -1.8132 REMARK 3 L13: 5.8164 L23: -2.2466 REMARK 3 S TENSOR REMARK 3 S11: 0.3282 S12: -0.0284 S13: -0.3338 REMARK 3 S21: -0.1360 S22: -0.0731 S23: 0.0667 REMARK 3 S31: 0.4247 S32: -0.1891 S33: -0.2303 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.5261 -1.2984 22.2618 REMARK 3 T TENSOR REMARK 3 T11: 0.0820 T22: 0.0840 REMARK 3 T33: 0.1194 T12: 0.0064 REMARK 3 T13: 0.0337 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 3.0564 L22: 1.0602 REMARK 3 L33: 3.2212 L12: -0.3246 REMARK 3 L13: 1.4308 L23: -0.4501 REMARK 3 S TENSOR REMARK 3 S11: 0.0380 S12: -0.0925 S13: -0.0688 REMARK 3 S21: -0.0342 S22: -0.0455 S23: 0.0017 REMARK 3 S31: 0.0708 S32: -0.0467 S33: 0.0070 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7592 7.5431 16.6908 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.2553 REMARK 3 T33: 0.2253 T12: 0.1001 REMARK 3 T13: 0.0163 T23: -0.0717 REMARK 3 L TENSOR REMARK 3 L11: 6.3809 L22: 4.2836 REMARK 3 L33: 4.8020 L12: 2.1126 REMARK 3 L13: 2.6995 L23: 0.9025 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: 0.0377 S13: 0.3794 REMARK 3 S21: -0.0538 S22: -0.2873 S23: 0.4568 REMARK 3 S31: -0.1088 S32: -0.6158 S33: 0.1096 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1248 6.5071 27.0960 REMARK 3 T TENSOR REMARK 3 T11: 0.1178 T22: 0.1206 REMARK 3 T33: 0.1217 T12: 0.0120 REMARK 3 T13: 0.0284 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 3.8035 L22: 2.4059 REMARK 3 L33: 3.9008 L12: -1.4136 REMARK 3 L13: 0.1172 L23: 1.0601 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: -0.3997 S13: 0.2628 REMARK 3 S21: 0.0756 S22: -0.1191 S23: 0.0557 REMARK 3 S31: -0.1341 S32: -0.3517 S33: 0.1313 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2727 -0.1293 12.3398 REMARK 3 T TENSOR REMARK 3 T11: 0.1877 T22: 0.3215 REMARK 3 T33: 0.2066 T12: 0.0507 REMARK 3 T13: 0.0833 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 3.3626 L22: 5.5309 REMARK 3 L33: 3.7408 L12: -1.7794 REMARK 3 L13: -1.7766 L23: 4.3458 REMARK 3 S TENSOR REMARK 3 S11: 0.1825 S12: 0.4936 S13: 0.1479 REMARK 3 S21: -0.6594 S22: 0.0503 S23: -0.6569 REMARK 3 S31: -0.2933 S32: 0.7159 S33: -0.2989 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1422 -9.7013 11.5430 REMARK 3 T TENSOR REMARK 3 T11: 0.2917 T22: 0.2687 REMARK 3 T33: 0.2113 T12: 0.0630 REMARK 3 T13: 0.0162 T23: -0.0646 REMARK 3 L TENSOR REMARK 3 L11: 1.0773 L22: 2.4071 REMARK 3 L33: 1.4975 L12: 0.7224 REMARK 3 L13: -1.0495 L23: -0.5446 REMARK 3 S TENSOR REMARK 3 S11: -0.0155 S12: 1.0018 S13: -0.4272 REMARK 3 S21: -0.5718 S22: 0.0452 S23: -0.1671 REMARK 3 S31: 0.6238 S32: 0.0781 S33: -0.0524 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0135 1.5523 4.6657 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.2239 REMARK 3 T33: 0.1641 T12: 0.0487 REMARK 3 T13: 0.0336 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.0283 L22: 6.1888 REMARK 3 L33: 2.2613 L12: 1.2784 REMARK 3 L13: 1.4180 L23: -0.0285 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: 0.2461 S13: 0.0562 REMARK 3 S21: -0.3825 S22: -0.1333 S23: -0.0768 REMARK 3 S31: 0.1115 S32: 0.1945 S33: 0.1459 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6749 3.8250 3.2345 REMARK 3 T TENSOR REMARK 3 T11: 0.2139 T22: 0.1471 REMARK 3 T33: 0.1270 T12: 0.0567 REMARK 3 T13: 0.0067 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 4.2097 L22: 7.8572 REMARK 3 L33: 6.8255 L12: 1.0395 REMARK 3 L13: 0.7179 L23: 5.2525 REMARK 3 S TENSOR REMARK 3 S11: -0.0747 S12: 0.3689 S13: -0.0827 REMARK 3 S21: -0.8077 S22: -0.1560 S23: -0.0113 REMARK 3 S31: -0.3852 S32: 0.0858 S33: 0.2535 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 6DP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41833 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 23.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 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 (%): 49.49 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 40.71300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.87350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.71300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.87350 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: 5270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 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: 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 HZ2 LYS A 127 O2 EDO A 213 1.59 REMARK 500 OE2 GLU A 96 O HOH A 301 2.04 REMARK 500 O HOH A 402 O HOH A 438 2.10 REMARK 500 CL CL A 203 O3 GOL A 212 2.12 REMARK 500 O HOH A 417 O HOH A 447 2.16 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 422 O HOH A 422 2656 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C b 5 P C b 5 OP3 -0.115 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. = 2.0 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 464 DISTANCE = 6.07 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 115.9 REMARK 620 3 HOH A 310 O 91.7 90.9 REMARK 620 4 HOH A 328 O 88.9 85.6 176.3 REMARK 620 5 C b 5 OP1 125.5 118.6 88.9 93.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 202 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 101.6 REMARK 620 3 ASP A 132 OD1 118.3 111.7 REMARK 620 4 U B 4 O3' 122.6 96.9 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG b 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 340 O REMARK 620 2 C b 5 OP3 92.2 REMARK 620 3 G b 6 OP2 88.2 95.2 REMARK 620 4 HOH b 201 O 173.4 89.7 97.9 REMARK 620 5 HOH b 205 O 84.3 86.5 172.4 89.5 REMARK 620 6 HOH b 207 O 91.7 172.5 91.2 85.7 87.5 REMARK 620 N 1 2 3 4 5 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 LI A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 PEG A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG 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 GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG b 101 DBREF 6DP8 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP8 B 1 4 PDB 6DP8 6DP8 1 4 DBREF 6DP8 b 5 6 PDB 6DP8 6DP8 5 6 DBREF 6DP8 C 1 6 PDB 6DP8 6DP8 1 6 SEQADV 6DP8 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP8 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP8 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP8 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 LI A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET GOL A 206 6 HET GOL A 207 6 HET EDO A 208 4 HET PEG A 209 7 HET PEG A 210 7 HET EDO A 211 4 HET GOL A 212 6 HET EDO A 213 4 HET EDO A 214 4 HET EDO A 215 4 HET EDO B 101 4 HET MG b 101 1 HETNAM MG MAGNESIUM ION HETNAM LI LITHIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 6 LI LI 1+ FORMUL 7 CL 3(CL 1-) FORMUL 10 GOL 3(C3 H8 O3) FORMUL 12 EDO 6(C2 H6 O2) FORMUL 13 PEG 2(C4 H10 O3) FORMUL 22 HOH *208(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 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.94 LINK OD1 ASP A 71 LI LI A 202 1555 1555 1.98 LINK OE1 GLU A 109 LI LI A 202 1555 1555 2.01 LINK OD1 ASP A 132 LI LI A 202 1555 1555 1.93 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.94 LINK MG MG A 201 O HOH A 310 1555 1555 2.11 LINK MG MG A 201 O HOH A 328 1555 1555 2.13 LINK MG MG A 201 OP1 C b 5 1555 1555 2.00 LINK LI LI A 202 O3' U B 4 1555 1555 1.99 LINK O HOH A 340 MG MG b 101 1555 1555 2.09 LINK OP3 C b 5 MG MG b 101 1555 1555 2.02 LINK OP2 G b 6 MG MG b 101 1555 1555 2.08 LINK MG MG b 101 O HOH b 201 1555 1555 2.02 LINK MG MG b 101 O HOH b 205 1555 1555 2.10 LINK MG MG b 101 O HOH b 207 1555 1555 2.06 CISPEP 1 ASN A 77 PRO A 78 0 -1.55 SITE 1 AC1 5 ASP A 71 ASP A 192 HOH A 310 HOH A 328 SITE 2 AC1 5 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 2 TYR A 83 GOL A 212 SITE 1 AC4 1 HOH A 365 SITE 1 AC5 3 ILE A 64 HOH A 430 HOH A 464 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 351 HOH A 366 SITE 3 AC6 9 HOH A 369 SITE 1 AC7 6 GLY A 76 ASN A 77 A B 1 DG C 2 SITE 2 AC7 6 DA C 3 G b 6 SITE 1 AC8 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AC9 5 VAL A 150 ASN A 152 GLU A 154 HOH A 403 SITE 2 AC9 5 HOH C 103 SITE 1 AD1 9 ILE A 63 TRP A 65 VAL A 150 ARG A 151 SITE 2 AD1 9 TRP A 181 TRP A 186 LYS A 190 HOH A 315 SITE 3 AD1 9 HOH A 414 SITE 1 AD2 5 ARG A 97 LEU A 157 LEU A 161 THR A 173 SITE 2 AD2 5 HOH A 387 SITE 1 AD3 9 HIS A 115 ARG A 118 CL A 203 HOH A 304 SITE 2 AD3 9 HOH A 306 HOH A 341 HOH A 351 HOH A 367 SITE 3 AD3 9 HOH A 387 SITE 1 AD4 5 GLU A 66 LEU A 94 LYS A 127 HOH A 329 SITE 2 AD4 5 HOH A 371 SITE 1 AD5 5 THR A 148 HOH A 307 HOH A 357 DT C 4 SITE 2 AD5 5 DG C 5 SITE 1 AD6 7 SER A 147 THR A 148 LEU A 149 VAL A 150 SITE 2 AD6 7 ARG A 151 HOH A 388 HOH A 420 SITE 1 AD7 3 ARG A 195 A B 1 G b 6 SITE 1 AD8 6 HOH A 340 C b 5 G b 6 HOH b 201 SITE 2 AD8 6 HOH b 205 HOH b 207 CRYST1 81.426 37.747 61.811 90.00 95.45 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 0.012281 0.000000 0.001172 0.00000 SCALE2 0.000000 0.026492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016252 0.00000