HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOK 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 1) 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 6DOK 1 LINK REVDAT 1 15-AUG-18 6DOK 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. 1.38 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 36821 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) : 0.149 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 : 1830 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 19.9524 - 3.2314 0.93 2734 157 0.1188 0.1357 REMARK 3 2 3.2314 - 2.5666 1.00 2883 150 0.1392 0.1605 REMARK 3 3 2.5666 - 2.2427 1.00 2830 169 0.1430 0.1666 REMARK 3 4 2.2427 - 2.0378 1.00 2856 146 0.1456 0.1680 REMARK 3 5 2.0378 - 1.8919 1.00 2865 147 0.1591 0.1731 REMARK 3 6 1.8919 - 1.7804 1.00 2812 156 0.1747 0.2168 REMARK 3 7 1.7804 - 1.6913 1.00 2861 140 0.1752 0.2241 REMARK 3 8 1.6913 - 1.6177 1.00 2828 148 0.1850 0.2183 REMARK 3 9 1.6177 - 1.5555 1.00 2830 125 0.2095 0.2337 REMARK 3 10 1.5555 - 1.5018 0.98 2771 158 0.2350 0.2684 REMARK 3 11 1.5018 - 1.4549 0.95 2709 128 0.2614 0.2820 REMARK 3 12 1.4549 - 1.4133 0.89 2526 123 0.2988 0.3440 REMARK 3 13 1.4133 - 1.3761 0.53 1486 83 0.3190 0.3658 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) : 21.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.93 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 1462 REMARK 3 ANGLE : 1.001 2022 REMARK 3 CHIRALITY : 0.070 220 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 23.911 575 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): 40.8080 -4.2353 18.8923 REMARK 3 T TENSOR REMARK 3 T11: 0.2149 T22: 0.5871 REMARK 3 T33: 0.3481 T12: 0.0873 REMARK 3 T13: 0.0491 T23: 0.0403 REMARK 3 L TENSOR REMARK 3 L11: 4.8868 L22: 3.3985 REMARK 3 L33: 5.7377 L12: -0.9842 REMARK 3 L13: -5.0663 L23: -0.2256 REMARK 3 S TENSOR REMARK 3 S11: 0.1185 S12: 0.4124 S13: 0.0650 REMARK 3 S21: -0.2326 S22: -0.3597 S23: -0.5998 REMARK 3 S31: 0.1214 S32: 1.9268 S33: 0.3522 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4891 -6.4855 16.5211 REMARK 3 T TENSOR REMARK 3 T11: 0.1880 T22: 0.1811 REMARK 3 T33: 0.2038 T12: -0.0006 REMARK 3 T13: -0.0053 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 3.9162 L22: 2.5606 REMARK 3 L33: 7.7899 L12: -1.9109 REMARK 3 L13: 5.4689 L23: -2.1880 REMARK 3 S TENSOR REMARK 3 S11: 0.4482 S12: 0.0821 S13: -0.4811 REMARK 3 S21: -0.2404 S22: -0.1053 S23: 0.1278 REMARK 3 S31: 0.5581 S32: -0.1982 S33: -0.3484 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9854 -11.5909 24.0163 REMARK 3 T TENSOR REMARK 3 T11: 0.2491 T22: 0.2287 REMARK 3 T33: 0.3729 T12: 0.0492 REMARK 3 T13: -0.0216 T23: 0.0516 REMARK 3 L TENSOR REMARK 3 L11: 4.3401 L22: 5.3614 REMARK 3 L33: 8.6115 L12: -0.8704 REMARK 3 L13: -5.8238 L23: 0.5654 REMARK 3 S TENSOR REMARK 3 S11: -0.0406 S12: -0.6979 S13: -0.8835 REMARK 3 S21: 0.1169 S22: 0.0665 S23: -0.5395 REMARK 3 S31: 0.8673 S32: 0.4629 S33: 0.0612 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9495 -0.9566 23.3531 REMARK 3 T TENSOR REMARK 3 T11: 0.1026 T22: 0.1563 REMARK 3 T33: 0.1621 T12: 0.0154 REMARK 3 T13: 0.0272 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 4.5082 L22: 0.9658 REMARK 3 L33: 4.8255 L12: -0.4728 REMARK 3 L13: 3.0031 L23: -0.0396 REMARK 3 S TENSOR REMARK 3 S11: 0.0800 S12: -0.4008 S13: -0.1228 REMARK 3 S21: -0.0325 S22: -0.0425 S23: 0.0613 REMARK 3 S31: 0.0617 S32: -0.4583 S33: -0.0180 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9759 9.3898 16.5905 REMARK 3 T TENSOR REMARK 3 T11: 0.3079 T22: 0.1566 REMARK 3 T33: 0.2579 T12: -0.0013 REMARK 3 T13: 0.0155 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 7.6321 L22: 7.5662 REMARK 3 L33: 8.4613 L12: -4.0316 REMARK 3 L13: 1.1147 L23: 2.2822 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: 0.1707 S13: 0.7607 REMARK 3 S21: -0.2119 S22: -0.2562 S23: -0.3952 REMARK 3 S31: -1.1631 S32: 0.0730 S33: 0.1208 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7592 7.8212 16.0468 REMARK 3 T TENSOR REMARK 3 T11: 0.3493 T22: 0.4926 REMARK 3 T33: 0.2651 T12: 0.2826 REMARK 3 T13: -0.0159 T23: -0.0878 REMARK 3 L TENSOR REMARK 3 L11: 8.7940 L22: 2.1962 REMARK 3 L33: 3.1427 L12: 0.4850 REMARK 3 L13: 2.6964 L23: -0.9622 REMARK 3 S TENSOR REMARK 3 S11: 0.1552 S12: -0.1840 S13: 0.4848 REMARK 3 S21: -0.1216 S22: -0.3328 S23: 0.4777 REMARK 3 S31: -0.5323 S32: -1.0346 S33: 0.0875 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4355 5.7523 24.8976 REMARK 3 T TENSOR REMARK 3 T11: 0.1912 T22: 0.3840 REMARK 3 T33: 0.2233 T12: 0.1107 REMARK 3 T13: 0.0263 T23: -0.0435 REMARK 3 L TENSOR REMARK 3 L11: 4.0259 L22: 2.0420 REMARK 3 L33: 8.2594 L12: 0.6471 REMARK 3 L13: 5.7581 L23: 1.1072 REMARK 3 S TENSOR REMARK 3 S11: 0.1496 S12: -0.4781 S13: 0.1044 REMARK 3 S21: -0.0439 S22: -0.2419 S23: 0.1537 REMARK 3 S31: -0.3197 S32: -1.0281 S33: 0.0594 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9797 8.3948 30.4948 REMARK 3 T TENSOR REMARK 3 T11: 0.2198 T22: 0.2558 REMARK 3 T33: 0.2459 T12: 0.0106 REMARK 3 T13: -0.0062 T23: -0.0389 REMARK 3 L TENSOR REMARK 3 L11: 4.6208 L22: 7.5813 REMARK 3 L33: 9.2899 L12: -5.3859 REMARK 3 L13: -6.1550 L23: 5.9828 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: -0.6242 S13: 0.5732 REMARK 3 S21: 0.0148 S22: 0.2654 S23: -0.4046 REMARK 3 S31: -0.5396 S32: 0.2434 S33: -0.2859 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5755 -0.8875 12.3173 REMARK 3 T TENSOR REMARK 3 T11: 0.2318 T22: 0.3841 REMARK 3 T33: 0.2500 T12: 0.0788 REMARK 3 T13: 0.0920 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 3.8593 L22: 8.2046 REMARK 3 L33: 8.4090 L12: -0.4344 REMARK 3 L13: -0.5835 L23: 5.4688 REMARK 3 S TENSOR REMARK 3 S11: 0.3247 S12: 0.6938 S13: 0.0125 REMARK 3 S21: -0.8201 S22: -0.1575 S23: -0.7483 REMARK 3 S31: -0.1473 S32: 0.5651 S33: -0.1754 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4066 -9.5215 12.3433 REMARK 3 T TENSOR REMARK 3 T11: 0.3600 T22: 0.3009 REMARK 3 T33: 0.2896 T12: 0.0795 REMARK 3 T13: -0.0268 T23: -0.0679 REMARK 3 L TENSOR REMARK 3 L11: 8.6249 L22: 2.2165 REMARK 3 L33: 8.8396 L12: 2.5840 REMARK 3 L13: -5.6839 L23: 0.3539 REMARK 3 S TENSOR REMARK 3 S11: 0.1071 S12: 0.9434 S13: -0.5602 REMARK 3 S21: -0.3715 S22: -0.0933 S23: 0.1365 REMARK 3 S31: 0.9747 S32: -0.1757 S33: 0.0312 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): 23.8170 1.1860 4.5340 REMARK 3 T TENSOR REMARK 3 T11: 0.3350 T22: 0.2862 REMARK 3 T33: 0.1934 T12: 0.0941 REMARK 3 T13: 0.0505 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 5.2572 L22: 5.0142 REMARK 3 L33: 5.3027 L12: -0.4309 REMARK 3 L13: 3.1446 L23: -2.5114 REMARK 3 S TENSOR REMARK 3 S11: 0.0360 S12: 0.6000 S13: -0.1143 REMARK 3 S21: -0.6754 S22: -0.2875 S23: -0.2327 REMARK 3 S31: 0.1080 S32: 0.3640 S33: 0.3432 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4562 3.6811 3.2075 REMARK 3 T TENSOR REMARK 3 T11: 0.4075 T22: 0.2014 REMARK 3 T33: 0.1625 T12: 0.1225 REMARK 3 T13: -0.0291 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 5.1301 L22: 5.2158 REMARK 3 L33: 9.9178 L12: 0.0558 REMARK 3 L13: -1.1587 L23: 3.8266 REMARK 3 S TENSOR REMARK 3 S11: -0.0377 S12: 0.3962 S13: -0.2159 REMARK 3 S21: -1.1465 S22: -0.3232 S23: 0.2203 REMARK 3 S31: -0.4707 S32: -0.3439 S33: 0.4046 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 6DOK 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_1000234978. 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 : 36837 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 19.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.9 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 40.80850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.71650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.80850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.71650 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: 7880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 432 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 OE2 GLU A 154 O HOH A 301 2.10 REMARK 500 OG1 THR A 90 O HOH A 302 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 416 O HOH A 416 2656 1.76 REMARK 500 O HOH A 410 O HOH A 458 3545 2.10 REMARK 500 OE2 GLU A 175 O HOH A 416 2656 2.17 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' -0.042 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. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 460 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 461 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 462 DISTANCE = 7.43 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 98.2 REMARK 620 3 HOH A 312 O 89.2 92.9 REMARK 620 4 HOH A 320 O 173.4 77.8 85.8 REMARK 620 5 C b 5 OP1 102.3 157.8 95.8 82.5 REMARK 620 6 HOH b 101 O 88.2 91.2 175.4 97.1 81.1 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 133.6 96.5 REMARK 620 4 ASP A 132 OD2 108.2 145.4 49.7 REMARK 620 5 U B 4 O3' 136.6 86.0 86.7 84.8 REMARK 620 6 C b 5 OP1 82.0 113.3 128.4 88.7 56.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 HOH A 312 O 57.7 REMARK 620 3 HOH A 320 O 52.4 58.9 REMARK 620 4 HOH A 324 O 66.0 114.2 60.8 REMARK 620 5 G b 6 OP2 101.4 54.2 61.6 113.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 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 A 211 DBREF 6DOK A 61 195 UNP Q9KEI9 RNH1_BACHD 61 195 DBREF 6DOK B 1 4 PDB 6DOK 6DOK 1 4 DBREF 6DOK b 5 6 PDB 6DOK 6DOK 5 6 DBREF 6DOK C 1 6 PDB 6DOK 6DOK 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 A 211 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 1.60 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.02 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.16 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.27 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.25 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.81 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.97 LINK OD1 ASP A 192 K K A 203 1555 1555 3.04 LINK MG MG A 201 O HOH A 312 1555 1555 2.06 LINK MG MG A 201 O HOH A 320 1555 1555 2.23 LINK MG MG A 201 OP1 C b 5 1555 1555 2.08 LINK MG MG A 201 O HOH b 101 1555 1555 2.09 LINK MG MG A 202 O3' U B 4 1555 1555 2.68 LINK MG MG A 202 OP1 C b 5 1555 1555 2.54 LINK K K A 203 O HOH A 312 1555 1555 3.00 LINK K K A 203 O HOH A 320 1555 1555 2.94 LINK K K A 203 O HOH A 324 1555 1555 2.97 LINK K K A 203 OP2 G b 6 1555 1555 3.00 CISPEP 1 ASN A 77 PRO A 78 0 1.03 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 312 HOH A 320 SITE 2 AC1 6 C b 5 HOH b 101 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 312 HOH A 320 HOH A 324 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 456 HOH A 460 SITE 1 AC6 6 GLY A 76 ASN A 77 PRO A 78 HOH B 108 SITE 2 AC6 6 DG C 2 DA C 3 SITE 1 AC7 6 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AC7 6 ASN A 170 HOH A 307 SITE 1 AC8 8 GLU A 66 LEU A 94 ARG A 123 SER A 125 SITE 2 AC8 8 LYS A 127 HOH A 306 HOH A 335 HOH A 399 SITE 1 AC9 4 LYS A 143 THR A 173 TYR A 174 HOH A 375 SITE 1 AD1 4 LYS A 89 GLU A 153 ALA A 156 HOH A 439 SITE 1 AD2 6 THR A 148 HOH A 304 HOH A 379 DT C 4 SITE 2 AD2 6 DG C 5 HOH C 107 CRYST1 81.617 37.433 62.249 90.00 96.58 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 0.012252 0.000000 0.001414 0.00000 SCALE2 0.000000 0.026714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016171 0.00000