HEADER HYDROLASE/RNA/DNA 09-JUN-18 6DPI TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 K196A IN TITLE 2 COMPLEX WITH AN RNA/DNA HYBRID: REACTION IN 10 MM MG2+ AND 200 MM RB+ TITLE 3 FOR 40 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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF INTACT RNA (5'- COMPND 11 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF INTACT RNA (5'- COMPND 16 R(*AP*CP*AP*UP*CP*G)-3'); COMPND 17 CHAIN: b; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 21 CHAIN: C; COMPND 22 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_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 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-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DPI 1 LINK REVDAT 1 15-AUG-18 6DPI 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. 1.35 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 39993 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1953 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 19.9830 - 3.2422 0.99 2899 141 0.1168 0.1450 REMARK 3 2 3.2422 - 2.5751 0.99 2799 157 0.1392 0.1827 REMARK 3 3 2.5751 - 2.2501 0.99 2779 142 0.1381 0.1547 REMARK 3 4 2.2501 - 2.0446 0.98 2758 157 0.1342 0.1685 REMARK 3 5 2.0446 - 1.8982 0.98 2778 144 0.1425 0.1819 REMARK 3 6 1.8982 - 1.7863 0.98 2701 148 0.1493 0.1683 REMARK 3 7 1.7863 - 1.6969 0.97 2737 130 0.1471 0.1755 REMARK 3 8 1.6969 - 1.6231 0.97 2711 167 0.1539 0.1751 REMARK 3 9 1.6231 - 1.5606 0.97 2730 129 0.1736 0.2110 REMARK 3 10 1.5606 - 1.5068 0.96 2717 114 0.1855 0.2150 REMARK 3 11 1.5068 - 1.4597 0.96 2711 125 0.2163 0.2402 REMARK 3 12 1.4597 - 1.4180 0.96 2658 143 0.2468 0.2447 REMARK 3 13 1.4180 - 1.3807 0.95 2697 124 0.2693 0.2549 REMARK 3 14 1.3807 - 1.3470 0.85 2365 132 0.2991 0.2994 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1466 REMARK 3 ANGLE : 1.033 2022 REMARK 3 CHIRALITY : 0.072 221 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 22.262 571 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): 40.4850 -4.3226 18.9277 REMARK 3 T TENSOR REMARK 3 T11: 0.1859 T22: 0.4375 REMARK 3 T33: 0.3209 T12: 0.0734 REMARK 3 T13: 0.0635 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 6.5956 L22: 3.7118 REMARK 3 L33: 5.8678 L12: 1.8677 REMARK 3 L13: 1.5404 L23: -1.2623 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: 0.3646 S13: -0.0011 REMARK 3 S21: -0.3263 S22: -0.0994 S23: -0.9032 REMARK 3 S31: 0.0974 S32: 1.3664 S33: 0.2471 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7343 -6.0434 16.9312 REMARK 3 T TENSOR REMARK 3 T11: 0.1260 T22: 0.0869 REMARK 3 T33: 0.1545 T12: 0.0069 REMARK 3 T13: 0.0059 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 8.6103 L22: 2.1743 REMARK 3 L33: 8.4974 L12: -2.1427 REMARK 3 L13: 7.3537 L23: -2.1470 REMARK 3 S TENSOR REMARK 3 S11: 0.3051 S12: 0.1101 S13: -0.4644 REMARK 3 S21: -0.1621 S22: -0.0741 S23: 0.0963 REMARK 3 S31: 0.3333 S32: -0.0503 S33: -0.2965 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6254 -11.5488 24.0727 REMARK 3 T TENSOR REMARK 3 T11: 0.1986 T22: 0.1539 REMARK 3 T33: 0.2885 T12: 0.0244 REMARK 3 T13: -0.0179 T23: 0.0506 REMARK 3 L TENSOR REMARK 3 L11: 6.6235 L22: 7.7614 REMARK 3 L33: 8.7119 L12: -3.4406 REMARK 3 L13: -5.7469 L23: 0.5814 REMARK 3 S TENSOR REMARK 3 S11: -0.1260 S12: -0.4587 S13: -1.3428 REMARK 3 S21: 0.1313 S22: 0.0023 S23: -0.3468 REMARK 3 S31: 0.7067 S32: 0.3097 S33: 0.1123 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0945 -4.7933 18.5924 REMARK 3 T TENSOR REMARK 3 T11: 0.1311 T22: 0.2525 REMARK 3 T33: 0.1941 T12: -0.0434 REMARK 3 T13: -0.0076 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 6.9224 L22: 7.7557 REMARK 3 L33: 6.9693 L12: -0.7298 REMARK 3 L13: -0.2917 L23: -5.8817 REMARK 3 S TENSOR REMARK 3 S11: 0.0887 S12: -0.4917 S13: -0.4883 REMARK 3 S21: -0.0257 S22: 0.3591 S23: 0.6157 REMARK 3 S31: 0.1897 S32: -0.8661 S33: -0.4583 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.4371 2.2285 22.6642 REMARK 3 T TENSOR REMARK 3 T11: 0.0895 T22: 0.0755 REMARK 3 T33: 0.1264 T12: 0.0021 REMARK 3 T13: 0.0314 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 4.1992 L22: 1.1566 REMARK 3 L33: 4.3240 L12: -1.0998 REMARK 3 L13: 2.4475 L23: -0.0975 REMARK 3 S TENSOR REMARK 3 S11: 0.0204 S12: -0.1298 S13: 0.0434 REMARK 3 S21: -0.0359 S22: -0.0210 S23: 0.0057 REMARK 3 S31: -0.1484 S32: -0.0719 S33: -0.0125 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5729 7.9218 16.0715 REMARK 3 T TENSOR REMARK 3 T11: 0.2096 T22: 0.2653 REMARK 3 T33: 0.1969 T12: 0.1321 REMARK 3 T13: 0.0105 T23: -0.0586 REMARK 3 L TENSOR REMARK 3 L11: 7.4634 L22: 1.8819 REMARK 3 L33: 4.2597 L12: -2.0296 REMARK 3 L13: 1.2811 L23: -1.9845 REMARK 3 S TENSOR REMARK 3 S11: 0.1356 S12: -0.0203 S13: 0.4167 REMARK 3 S21: -0.1810 S22: -0.2031 S23: 0.4118 REMARK 3 S31: -0.3427 S32: -0.6827 S33: 0.0292 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3221 5.8212 24.9293 REMARK 3 T TENSOR REMARK 3 T11: 0.1354 T22: 0.2204 REMARK 3 T33: 0.1632 T12: 0.0551 REMARK 3 T13: 0.0222 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 7.4606 L22: 2.6675 REMARK 3 L33: 7.1639 L12: 2.4350 REMARK 3 L13: 6.7819 L23: 2.8596 REMARK 3 S TENSOR REMARK 3 S11: 0.1174 S12: -0.4666 S13: 0.0659 REMARK 3 S21: 0.0340 S22: -0.2044 S23: 0.1222 REMARK 3 S31: -0.1897 S32: -0.6762 S33: 0.0912 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.8487 8.3534 30.5448 REMARK 3 T TENSOR REMARK 3 T11: 0.1462 T22: 0.1773 REMARK 3 T33: 0.1856 T12: -0.0005 REMARK 3 T13: -0.0007 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 3.3950 L22: 7.5639 REMARK 3 L33: 8.7951 L12: -4.4792 REMARK 3 L13: -5.2074 L23: 5.7740 REMARK 3 S TENSOR REMARK 3 S11: 0.0345 S12: -0.6740 S13: 0.6224 REMARK 3 S21: -0.0543 S22: 0.3435 S23: -0.3536 REMARK 3 S31: -0.3849 S32: 0.4082 S33: -0.2406 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3278 -1.0334 12.3092 REMARK 3 T TENSOR REMARK 3 T11: 0.1575 T22: 0.2983 REMARK 3 T33: 0.1800 T12: 0.0601 REMARK 3 T13: 0.0701 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 2.1293 L22: 7.7853 REMARK 3 L33: 8.5691 L12: 0.3020 REMARK 3 L13: 0.1320 L23: 5.2012 REMARK 3 S TENSOR REMARK 3 S11: 0.2483 S12: 0.6557 S13: 0.0423 REMARK 3 S21: -0.5930 S22: -0.1651 S23: -0.5907 REMARK 3 S31: -0.0615 S32: 0.4346 S33: -0.1927 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2118 -9.6962 12.5224 REMARK 3 T TENSOR REMARK 3 T11: 0.3077 T22: 0.2260 REMARK 3 T33: 0.2388 T12: 0.0646 REMARK 3 T13: -0.0316 T23: -0.0818 REMARK 3 L TENSOR REMARK 3 L11: 8.5371 L22: 2.4039 REMARK 3 L33: 7.9306 L12: 3.0753 REMARK 3 L13: -6.2211 L23: -0.4611 REMARK 3 S TENSOR REMARK 3 S11: -0.1835 S12: 0.8647 S13: -0.7404 REMARK 3 S21: -0.5503 S22: -0.0047 S23: 0.2434 REMARK 3 S31: 0.6155 S32: -0.2131 S33: 0.2487 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.7096 1.3255 4.5826 REMARK 3 T TENSOR REMARK 3 T11: 0.2152 T22: 0.1857 REMARK 3 T33: 0.1438 T12: 0.0743 REMARK 3 T13: 0.0557 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 4.6385 L22: 6.5191 REMARK 3 L33: 3.3552 L12: 1.0759 REMARK 3 L13: 2.8797 L23: -0.1608 REMARK 3 S TENSOR REMARK 3 S11: -0.0463 S12: 0.3971 S13: 0.0340 REMARK 3 S21: -0.6731 S22: -0.2236 S23: -0.3213 REMARK 3 S31: 0.0167 S32: 0.3537 S33: 0.2632 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4106 3.8314 3.1640 REMARK 3 T TENSOR REMARK 3 T11: 0.2539 T22: 0.1402 REMARK 3 T33: 0.1289 T12: 0.0807 REMARK 3 T13: -0.0241 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 3.6421 L22: 4.1209 REMARK 3 L33: 7.2393 L12: -0.4726 REMARK 3 L13: -1.6601 L23: 2.8390 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: 0.3305 S13: -0.1113 REMARK 3 S21: -0.7439 S22: -0.3400 S23: 0.1786 REMARK 3 S31: -0.3341 S32: -0.3246 S33: 0.2934 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 6DPI 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_1000235033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 19.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.77300 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: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 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 40.81000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.81000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.64500 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: 5710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 O HOH A 415 O HOH A 459 2.06 REMARK 500 OH TYR A 174 O HOH A 301 2.08 REMARK 500 O HOH C 202 O HOH C 213 2.11 REMARK 500 OE2 GLU A 154 O HOH A 302 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 420 O HOH A 420 2656 1.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG C 2 O3' DG C 2 C3' -0.046 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 461 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 462 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 463 DISTANCE = 7.29 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 94.1 REMARK 620 3 HOH A 318 O 174.5 81.1 REMARK 620 4 HOH A 331 O 87.5 92.6 90.2 REMARK 620 5 HOH A 375 O 93.0 88.2 89.4 179.1 REMARK 620 6 C b 5 OP1 99.7 165.6 85.3 92.3 86.9 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 102.0 REMARK 620 3 GLU A 109 OE2 80.5 46.7 REMARK 620 4 ASP A 132 OD1 144.8 97.1 91.9 REMARK 620 5 ASP A 132 OD2 112.1 145.6 134.1 51.7 REMARK 620 6 HOH A 373 O 78.9 104.2 59.5 67.8 79.1 REMARK 620 7 U B 4 O3' 130.0 76.2 121.7 83.2 84.9 150.9 REMARK 620 8 C b 5 OP1 79.7 104.5 139.6 123.5 86.2 147.1 53.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RB A 204 RB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 121 O REMARK 620 2 ASN A 124 OD1 83.0 REMARK 620 3 HOH A 387 O 63.1 65.2 REMARK 620 4 HOH A 413 O 87.7 86.5 140.5 REMARK 620 5 HOH A 423 O 111.2 108.1 62.4 157.0 REMARK 620 6 HOH A 441 O 100.8 162.5 131.8 76.7 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RB A 203 RB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 195 N REMARK 620 2 ALA A 196 N 64.9 REMARK 620 3 ALA A 196 OXT 133.5 68.6 REMARK 620 4 HOH A 318 O 164.2 117.6 51.9 REMARK 620 5 HOH A 343 O 101.3 87.2 76.3 64.1 REMARK 620 6 G b 6 OP2 129.1 97.5 57.0 66.7 126.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RB C 101 RB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 5 O6 REMARK 620 2 HOH C 213 O 81.9 REMARK 620 3 HOH C 218 O 123.8 122.0 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 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 RB A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RB 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 CL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 RB C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 102 DBREF 6DPI A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DPI B 1 4 PDB 6DPI 6DPI 1 4 DBREF 6DPI b 5 6 PDB 6DPI 6DPI 5 6 DBREF 6DPI C 1 6 PDB 6DPI 6DPI 1 6 SEQADV 6DPI GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPI SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPI HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPI MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPI ALA A 196 UNP Q9KEI9 LYS 196 ENGINEERED MUTATION 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 ALA 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 RB A 203 1 HET RB A 204 1 HET CL A 205 1 HET CL A 206 1 HET CL A 207 1 HET GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET GOL A 211 6 HET EDO A 212 4 HET EDO A 213 4 HET RB C 101 1 HET EDO C 102 4 HETNAM MG MAGNESIUM ION HETNAM RB RUBIDIUM ION HETNAM CL CHLORIDE 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 RB 3(RB 1+) FORMUL 9 CL 3(CL 1-) FORMUL 12 GOL 4(C3 H8 O3) FORMUL 16 EDO 3(C2 H6 O2) FORMUL 20 HOH *203(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 HIS A 172 1 18 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 2.04 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.21 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.34 LINK OE2 GLU A 109 MG MG A 202 1555 1555 2.99 LINK O LYS A 121 RB RB A 204 1555 1555 2.85 LINK OD1 ASN A 124 RB RB A 204 1555 1555 2.81 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.24 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.69 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.03 LINK N ARG A 195 RB RB A 203 1555 1555 2.76 LINK N ALA A 196 RB RB A 203 1555 1555 2.53 LINK OXT ALA A 196 RB RB A 203 1555 1555 3.06 LINK MG MG A 201 O HOH A 318 1555 1555 2.12 LINK MG MG A 201 O HOH A 331 1555 1555 2.03 LINK MG MG A 201 O HOH A 375 1555 1555 2.07 LINK MG MG A 201 OP1 C b 5 1555 1555 2.13 LINK MG MG A 202 O HOH A 373 1555 1555 2.92 LINK MG MG A 202 O3' U B 4 1555 1555 2.80 LINK MG MG A 202 OP1 C b 5 1555 1555 2.59 LINK RB RB A 203 O HOH A 318 1555 1555 2.97 LINK RB RB A 203 O HOH A 343 1555 1555 2.45 LINK RB RB A 203 OP2 G b 6 1555 1555 3.11 LINK RB RB A 204 O HOH A 387 1555 1555 2.61 LINK RB RB A 204 O HOH A 413 1555 1555 2.73 LINK RB RB A 204 O HOH A 423 1555 1555 2.55 LINK RB RB A 204 O HOH A 441 1555 1555 2.64 LINK O6 DG C 5 RB RB C 101 1555 1555 2.67 LINK RB RB C 101 O HOH C 213 1555 1555 3.14 LINK RB RB C 101 O BHOH C 218 1555 1555 2.44 CISPEP 1 ASN A 77 PRO A 78 0 2.07 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 318 HOH A 331 SITE 2 AC1 6 HOH A 375 C b 5 SITE 1 AC2 6 ASP A 71 GLU A 109 ASP A 132 HOH A 373 SITE 2 AC2 6 U B 4 C b 5 SITE 1 AC3 7 ASP A 192 TYR A 193 ARG A 195 ALA A 196 SITE 2 AC3 7 HOH A 318 HOH A 343 G b 6 SITE 1 AC4 6 LYS A 121 ASN A 124 HOH A 387 HOH A 413 SITE 2 AC4 6 HOH A 423 HOH A 441 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 3 HOH A 357 HOH A 443 HOH A 455 SITE 1 AC7 3 EDO A 213 HOH A 458 HOH A 461 SITE 1 AC8 5 GLY A 76 ASN A 77 PRO A 78 DG C 2 SITE 2 AC8 5 DA C 3 SITE 1 AC9 8 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC9 8 GLU A 167 GOL A 211 HOH A 304 HOH A 363 SITE 1 AD1 6 GLU A 66 SER A 125 LYS A 127 HOH A 308 SITE 2 AD1 6 HOH A 310 HOH A 390 SITE 1 AD2 7 HIS A 115 ARG A 118 ASN A 170 GOL A 209 SITE 2 AD2 7 HOH A 388 HOH A 398 HOH A 422 SITE 1 AD3 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AD4 6 ARG A 126 GLU A 175 PRO A 177 CL A 207 SITE 2 AD4 6 HOH A 377 HOH A 463 SITE 1 AD5 3 DT C 4 DG C 5 HOH C 218 SITE 1 AD6 5 THR A 148 DT C 4 DG C 5 HOH C 202 SITE 2 AD6 5 HOH C 203 CRYST1 81.620 37.290 62.382 90.00 96.98 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 0.001500 0.00000 SCALE2 0.000000 0.026817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016150 0.00000