HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOL TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2 MM MG2+ AND 25 MM K+ FOR 120 S TITLE 3 AT 21 C (DATASET 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 61-196); COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF INTACT RNA (5'- COMPND 10 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF INTACT RNA (5'- COMPND 15 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 16 CHAIN: b; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 20 CHAIN: C; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA, BH0863; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DOL 1 LINK REVDAT 1 15-AUG-18 6DOL 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_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) : 20.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 33630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1644 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 20.0628 - 3.2755 0.99 2786 154 0.1197 0.1502 REMARK 3 2 3.2755 - 2.6017 1.00 2763 121 0.1389 0.1715 REMARK 3 3 2.6017 - 2.2733 1.00 2729 140 0.1454 0.1833 REMARK 3 4 2.2733 - 2.0657 0.99 2690 135 0.1555 0.1920 REMARK 3 5 2.0657 - 1.9178 0.99 2696 148 0.1724 0.1902 REMARK 3 6 1.9178 - 1.8048 0.99 2678 150 0.2005 0.2460 REMARK 3 7 1.8048 - 1.7144 0.99 2695 128 0.1761 0.2298 REMARK 3 8 1.7144 - 1.6398 0.99 2653 131 0.1876 0.2269 REMARK 3 9 1.6398 - 1.5767 0.98 2650 153 0.2053 0.2321 REMARK 3 10 1.5767 - 1.5224 0.98 2670 137 0.2355 0.2653 REMARK 3 11 1.5224 - 1.4748 0.98 2614 143 0.2722 0.3231 REMARK 3 12 1.4748 - 1.4326 0.87 2362 104 0.3131 0.3231 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1462 REMARK 3 ANGLE : 1.002 2022 REMARK 3 CHIRALITY : 0.069 220 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 24.137 575 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.9071 -4.2386 18.8538 REMARK 3 T TENSOR REMARK 3 T11: 0.2253 T22: 0.5630 REMARK 3 T33: 0.3431 T12: 0.0963 REMARK 3 T13: 0.0443 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 4.9884 L22: 9.3546 REMARK 3 L33: 4.6953 L12: -1.1146 REMARK 3 L13: -4.1508 L23: -0.7603 REMARK 3 S TENSOR REMARK 3 S11: 0.2060 S12: 0.5676 S13: 0.0431 REMARK 3 S21: -0.5221 S22: -0.4223 S23: -0.8343 REMARK 3 S31: 0.1454 S32: 1.9930 S33: 0.2550 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6058 -6.4440 16.5121 REMARK 3 T TENSOR REMARK 3 T11: 0.2080 T22: 0.2099 REMARK 3 T33: 0.2309 T12: -0.0000 REMARK 3 T13: -0.0090 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 9.7030 L22: 1.4715 REMARK 3 L33: 4.5451 L12: -2.2789 REMARK 3 L13: 6.5050 L23: -1.7870 REMARK 3 S TENSOR REMARK 3 S11: 0.4216 S12: 0.1711 S13: -0.5843 REMARK 3 S21: -0.2262 S22: -0.1138 S23: 0.1278 REMARK 3 S31: 0.4870 S32: -0.0625 S33: -0.3513 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0986 -11.5360 23.9651 REMARK 3 T TENSOR REMARK 3 T11: 0.2474 T22: 0.2522 REMARK 3 T33: 0.3780 T12: 0.0396 REMARK 3 T13: -0.0138 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 7.4199 L22: 2.1022 REMARK 3 L33: 5.0289 L12: -1.0168 REMARK 3 L13: -5.7512 L23: 0.7682 REMARK 3 S TENSOR REMARK 3 S11: -0.0403 S12: -0.4271 S13: -1.4190 REMARK 3 S21: 0.0453 S22: 0.0073 S23: -0.3857 REMARK 3 S31: 0.6951 S32: 0.2990 S33: 0.1140 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1003 -0.9491 23.3185 REMARK 3 T TENSOR REMARK 3 T11: 0.1189 T22: 0.1435 REMARK 3 T33: 0.1620 T12: 0.0137 REMARK 3 T13: 0.0273 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.7530 L22: 0.9610 REMARK 3 L33: 4.9066 L12: -0.2908 REMARK 3 L13: 3.1686 L23: -0.0050 REMARK 3 S TENSOR REMARK 3 S11: 0.0619 S12: -0.3524 S13: -0.0988 REMARK 3 S21: -0.0137 S22: -0.0352 S23: 0.0538 REMARK 3 S31: 0.0389 S32: -0.3797 S33: -0.0260 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.1042 9.3414 16.5954 REMARK 3 T TENSOR REMARK 3 T11: 0.3097 T22: 0.1531 REMARK 3 T33: 0.2498 T12: -0.0056 REMARK 3 T13: 0.0095 T23: 0.0367 REMARK 3 L TENSOR REMARK 3 L11: 6.9276 L22: 5.8361 REMARK 3 L33: 3.2074 L12: -3.6965 REMARK 3 L13: 1.9794 L23: 1.6040 REMARK 3 S TENSOR REMARK 3 S11: 0.0954 S12: 0.1440 S13: 0.7533 REMARK 3 S21: -0.0556 S22: -0.2359 S23: -0.3529 REMARK 3 S31: -1.0554 S32: 0.0704 S33: 0.1143 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8831 7.8053 16.0409 REMARK 3 T TENSOR REMARK 3 T11: 0.3294 T22: 0.4191 REMARK 3 T33: 0.2554 T12: 0.2230 REMARK 3 T13: 0.0039 T23: -0.0976 REMARK 3 L TENSOR REMARK 3 L11: 8.8760 L22: 2.1995 REMARK 3 L33: 5.0290 L12: -0.5626 REMARK 3 L13: 2.8987 L23: -2.2222 REMARK 3 S TENSOR REMARK 3 S11: 0.2035 S12: -0.2474 S13: 0.4922 REMARK 3 S21: -0.0414 S22: -0.3174 S23: 0.4767 REMARK 3 S31: -0.4812 S32: -1.0445 S33: 0.0770 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5984 5.7245 24.8562 REMARK 3 T TENSOR REMARK 3 T11: 0.1982 T22: 0.3326 REMARK 3 T33: 0.1993 T12: 0.0829 REMARK 3 T13: 0.0379 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 8.9200 L22: 2.4326 REMARK 3 L33: 6.9196 L12: 0.5002 REMARK 3 L13: 7.5929 L23: 1.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.1492 S12: -0.4554 S13: -0.0472 REMARK 3 S21: 0.0617 S22: -0.1802 S23: 0.0901 REMARK 3 S31: -0.1902 S32: -0.8297 S33: 0.0778 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1183 8.3409 30.4558 REMARK 3 T TENSOR REMARK 3 T11: 0.2572 T22: 0.2489 REMARK 3 T33: 0.2672 T12: 0.0198 REMARK 3 T13: 0.0002 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 5.1111 L22: 4.5426 REMARK 3 L33: 6.3324 L12: -4.8264 REMARK 3 L13: -5.0692 L23: 4.9013 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: -0.9257 S13: 0.8489 REMARK 3 S21: 0.0359 S22: 0.3682 S23: -0.5309 REMARK 3 S31: -0.4419 S32: 0.4592 S33: -0.2722 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.6774 -0.8919 12.3129 REMARK 3 T TENSOR REMARK 3 T11: 0.2411 T22: 0.3965 REMARK 3 T33: 0.2448 T12: 0.0802 REMARK 3 T13: 0.0907 T23: 0.0484 REMARK 3 L TENSOR REMARK 3 L11: 3.6971 L22: 7.1423 REMARK 3 L33: 3.8586 L12: -0.8740 REMARK 3 L13: -0.6806 L23: 4.7318 REMARK 3 S TENSOR REMARK 3 S11: 0.2891 S12: 0.7514 S13: 0.0025 REMARK 3 S21: -0.6775 S22: -0.1970 S23: -0.7434 REMARK 3 S31: -0.0483 S32: 0.6828 S33: -0.2117 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4963 -9.4726 12.3434 REMARK 3 T TENSOR REMARK 3 T11: 0.3480 T22: 0.2962 REMARK 3 T33: 0.2804 T12: 0.0821 REMARK 3 T13: -0.0328 T23: -0.0632 REMARK 3 L TENSOR REMARK 3 L11: 3.3584 L22: 8.0991 REMARK 3 L33: 7.4341 L12: 2.0463 REMARK 3 L13: -4.6184 L23: -0.0110 REMARK 3 S TENSOR REMARK 3 S11: 0.1060 S12: 0.9268 S13: -0.3885 REMARK 3 S21: -0.5080 S22: -0.1128 S23: 0.3725 REMARK 3 S31: 0.7795 S32: -0.1504 S33: 0.0089 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN 'B' AND (RESID 1 THROUGH 4)) OR (CHAIN 'B' REMARK 3 AND (RESID 5 THROUGH 6)) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8937 1.1907 4.5362 REMARK 3 T TENSOR REMARK 3 T11: 0.3365 T22: 0.2785 REMARK 3 T33: 0.2047 T12: 0.0863 REMARK 3 T13: 0.0518 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 5.0465 L22: 1.9306 REMARK 3 L33: 4.8219 L12: -0.3886 REMARK 3 L13: 2.8615 L23: -2.1154 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: 0.5422 S13: -0.0654 REMARK 3 S21: -0.6936 S22: -0.3399 S23: -0.2815 REMARK 3 S31: 0.1833 S32: 0.3712 S33: 0.2735 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5438 3.6713 3.2369 REMARK 3 T TENSOR REMARK 3 T11: 0.3977 T22: 0.2162 REMARK 3 T33: 0.1800 T12: 0.1199 REMARK 3 T13: -0.0110 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 5.0469 L22: 5.6177 REMARK 3 L33: 9.8120 L12: -0.1225 REMARK 3 L13: -1.2772 L23: 3.7343 REMARK 3 S TENSOR REMARK 3 S11: -0.0440 S12: 0.3617 S13: -0.2225 REMARK 3 S21: -1.1212 S22: -0.3885 S23: 0.2348 REMARK 3 S31: -0.3896 S32: -0.4206 S33: 0.4270 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 6DOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33645 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 20.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 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 (%) : 79.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM REMARK 280 POTASSIUM IODIDE, 5 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.90050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.55650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.90050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.55650 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: 4870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7850 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 436 LIES ON A SPECIAL POSITION. 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 O HOH A 415 O HOH A 461 2.03 REMARK 500 OE2 GLU A 154 O HOH A 301 2.12 REMARK 500 OH TYR A 174 O HOH A 302 2.14 REMARK 500 O2 GOL C 101 O HOH C 201 2.14 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 1.77 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 2 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 463 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 464 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 7.37 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 99.2 REMARK 620 3 HOH A 310 O 174.2 75.2 REMARK 620 4 HOH A 319 O 91.6 93.7 87.6 REMARK 620 5 HOH A 351 O 86.3 89.1 94.7 176.7 REMARK 620 6 C b 5 OP1 102.6 155.9 83.2 95.9 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 101.4 REMARK 620 3 ASP A 132 OD1 133.0 95.1 REMARK 620 4 ASP A 132 OD2 109.5 143.6 49.6 REMARK 620 5 U B 4 O3' 139.3 84.5 85.5 84.4 REMARK 620 6 C b 5 OP1 83.7 113.2 128.8 89.3 57.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 HOH A 310 O 50.9 REMARK 620 3 HOH A 319 O 58.2 60.5 REMARK 620 4 HOH A 322 O 64.7 59.2 114.2 REMARK 620 5 G b 6 OP2 102.5 64.6 55.2 114.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD 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 GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 DBREF 6DOL A 61 195 UNP Q9KEI9 RNH1_BACHD 61 195 DBREF 6DOL B 1 4 PDB 6DOL 6DOL 1 4 DBREF 6DOL b 5 6 PDB 6DOL 6DOL 5 6 DBREF 6DOL C 1 6 PDB 6DOL 6DOL 1 6 SEQRES 1 A 135 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 135 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 135 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 135 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 135 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 135 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 135 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 135 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 135 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 135 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 135 ALA ASP TYR GLY ARG SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET GOL A 206 6 HET GOL A 207 6 HET GOL A 208 6 HET EDO A 209 4 HET EDO A 210 4 HET GOL C 101 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K K 1+ FORMUL 8 IOD 2(I 1-) FORMUL 10 GOL 4(C3 H8 O3) FORMUL 13 EDO 2(C2 H6 O2) FORMUL 16 HOH *201(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 ASN A 152 GLU A 154 5 3 HELIX 4 AA4 THR A 155 ASN A 170 1 16 HELIX 5 AA5 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 5 VAL A 93 GLY A 103 0 SHEET 2 AA1 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 AA1 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA1 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA1 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' U B 4 P C b 5 1555 1555 1.59 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.02 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.14 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.25 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.33 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.80 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.96 LINK OD1 ASP A 192 K K A 203 1555 1555 3.05 LINK MG MG A 201 O HOH A 310 1555 1555 2.25 LINK MG MG A 201 O HOH A 319 1555 1555 2.03 LINK MG MG A 201 O HOH A 351 1555 1555 2.18 LINK MG MG A 201 OP1 C b 5 1555 1555 2.05 LINK MG MG A 202 O3' U B 4 1555 1555 2.68 LINK MG MG A 202 OP1 C b 5 1555 1555 2.51 LINK K K A 203 O HOH A 310 1555 1555 2.94 LINK K K A 203 O HOH A 319 1555 1555 2.93 LINK K K A 203 O HOH A 322 1555 1555 2.99 LINK K K A 203 OP2 G b 6 1555 1555 3.00 CISPEP 1 ASN A 77 PRO A 78 0 -0.22 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 310 HOH A 319 SITE 2 AC1 6 HOH A 351 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 8 ASP A 192 TYR A 193 GLY A 194 ARG A 195 SITE 2 AC3 8 HOH A 310 HOH A 319 HOH A 322 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 460 HOH A 463 SITE 1 AC6 6 GLY A 76 ASN A 77 PRO A 78 HOH B 107 SITE 2 AC6 6 DG C 2 DA C 3 SITE 1 AC7 7 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC7 7 GLU A 167 ASN A 170 HOH A 307 SITE 1 AC8 7 GLU A 66 LEU A 94 ARG A 123 LYS A 127 SITE 2 AC8 7 HOH A 303 HOH A 312 HOH A 407 SITE 1 AC9 5 LYS A 143 THR A 173 TYR A 174 HOH A 378 SITE 2 AC9 5 HOH A 414 SITE 1 AD1 3 LYS A 89 GLU A 153 HOH A 443 SITE 1 AD2 6 THR A 148 DT C 4 DG C 5 HOH C 201 SITE 2 AD2 6 HOH C 204 HOH C 214 CRYST1 81.801 37.113 62.105 90.00 96.44 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 0.012225 0.000000 0.001380 0.00000 SCALE2 0.000000 0.026945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016204 0.00000