HEADER HYDROLASE/RNA/DNA 09-JUN-18 6DOH TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: SOAK IN 0.5 MM EGTA AND 200 MM K+ 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: 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 (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 6 GENE: RNHA, BH0863; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 15 ORGANISM_TAXID: 32644; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 19 ORGANISM_TAXID: 32644; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 23 ORGANISM_TAXID: 32644 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 6DOH 1 LINK REVDAT 1 15-AUG-18 6DOH 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. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 38054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 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 19.8160 - 3.2008 0.96 2897 174 0.1322 0.1628 REMARK 3 2 3.2008 - 2.5422 0.99 2935 160 0.1587 0.1890 REMARK 3 3 2.5422 - 2.2214 1.00 2925 149 0.1600 0.2143 REMARK 3 4 2.2214 - 2.0185 1.00 2945 140 0.1601 0.2084 REMARK 3 5 2.0185 - 1.8739 0.99 2918 136 0.1702 0.2093 REMARK 3 6 1.8739 - 1.7635 1.00 2942 151 0.1769 0.1846 REMARK 3 7 1.7635 - 1.6752 0.99 2889 160 0.1775 0.2277 REMARK 3 8 1.6752 - 1.6024 0.99 2885 158 0.2062 0.2360 REMARK 3 9 1.6024 - 1.5407 0.99 2899 136 0.2260 0.2582 REMARK 3 10 1.5407 - 1.4875 0.97 2818 141 0.2611 0.2975 REMARK 3 11 1.4875 - 1.4410 0.92 2696 129 0.2935 0.3547 REMARK 3 12 1.4410 - 1.3999 0.84 2407 132 0.3283 0.3279 REMARK 3 13 1.3999 - 1.3630 0.69 2024 108 0.3478 0.3349 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.46 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 1461 REMARK 3 ANGLE : 0.993 2027 REMARK 3 CHIRALITY : 0.068 222 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 24.056 578 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): 40.6835 -3.9585 18.8081 REMARK 3 T TENSOR REMARK 3 T11: 0.1962 T22: 0.4854 REMARK 3 T33: 0.3665 T12: 0.0970 REMARK 3 T13: 0.0751 T23: 0.0287 REMARK 3 L TENSOR REMARK 3 L11: 4.1047 L22: 5.3792 REMARK 3 L33: 7.5456 L12: 2.6624 REMARK 3 L13: 2.4393 L23: -2.0662 REMARK 3 S TENSOR REMARK 3 S11: 0.0504 S12: 0.9497 S13: 0.0797 REMARK 3 S21: -0.7025 S22: -0.5226 S23: -1.1070 REMARK 3 S31: 0.1244 S32: 1.0672 S33: 0.4136 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0884 -6.2577 16.5975 REMARK 3 T TENSOR REMARK 3 T11: 0.1738 T22: 0.2086 REMARK 3 T33: 0.1686 T12: -0.0005 REMARK 3 T13: -0.0208 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.8001 L22: 1.6062 REMARK 3 L33: 4.0586 L12: -0.1866 REMARK 3 L13: 3.3130 L23: 0.2587 REMARK 3 S TENSOR REMARK 3 S11: 0.2936 S12: 0.1895 S13: -0.3833 REMARK 3 S21: -0.1853 S22: -0.1370 S23: 0.0382 REMARK 3 S31: 0.3470 S32: -0.1429 S33: -0.2322 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8245 -6.2970 16.4267 REMARK 3 T TENSOR REMARK 3 T11: 0.1796 T22: 0.2060 REMARK 3 T33: 0.1615 T12: 0.0046 REMARK 3 T13: 0.0049 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 6.0600 L22: 2.3669 REMARK 3 L33: 5.5722 L12: -1.1557 REMARK 3 L13: 5.1927 L23: -2.1209 REMARK 3 S TENSOR REMARK 3 S11: 0.4181 S12: 0.2727 S13: -0.3364 REMARK 3 S21: -0.1874 S22: -0.2708 S23: 0.0856 REMARK 3 S31: 0.4656 S32: 0.0271 S33: -0.1748 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4144 -11.4504 23.7165 REMARK 3 T TENSOR REMARK 3 T11: 0.2383 T22: 0.2195 REMARK 3 T33: 0.3286 T12: 0.0270 REMARK 3 T13: -0.0026 T23: 0.0394 REMARK 3 L TENSOR REMARK 3 L11: 6.5331 L22: 4.3923 REMARK 3 L33: 3.9746 L12: 0.3508 REMARK 3 L13: -5.0776 L23: 0.0805 REMARK 3 S TENSOR REMARK 3 S11: -0.2256 S12: -0.2376 S13: -1.3485 REMARK 3 S21: 0.0294 S22: 0.0269 S23: -0.5374 REMARK 3 S31: 0.6090 S32: 0.3411 S33: 0.2035 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3830 0.8242 22.0848 REMARK 3 T TENSOR REMARK 3 T11: 0.0970 T22: 0.0982 REMARK 3 T33: 0.1153 T12: 0.0094 REMARK 3 T13: 0.0233 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 3.8637 L22: 0.8726 REMARK 3 L33: 4.3175 L12: -0.3895 REMARK 3 L13: 2.1764 L23: 0.0672 REMARK 3 S TENSOR REMARK 3 S11: 0.0159 S12: -0.1264 S13: -0.0737 REMARK 3 S21: -0.0398 S22: -0.0365 S23: -0.0209 REMARK 3 S31: -0.0708 S32: -0.1569 S33: 0.0361 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6115 7.9105 16.4465 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.3859 REMARK 3 T33: 0.2161 T12: 0.2154 REMARK 3 T13: -0.0255 T23: -0.1133 REMARK 3 L TENSOR REMARK 3 L11: 6.8278 L22: 2.8026 REMARK 3 L33: 4.6141 L12: -0.0567 REMARK 3 L13: 2.6580 L23: -0.0953 REMARK 3 S TENSOR REMARK 3 S11: 0.1374 S12: -0.0253 S13: 0.3587 REMARK 3 S21: -0.1964 S22: -0.3767 S23: 0.5230 REMARK 3 S31: -0.5270 S32: -0.8759 S33: 0.1128 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4222 5.7695 24.7934 REMARK 3 T TENSOR REMARK 3 T11: 0.1562 T22: 0.3071 REMARK 3 T33: 0.1738 T12: 0.0566 REMARK 3 T13: 0.0118 T23: -0.0564 REMARK 3 L TENSOR REMARK 3 L11: 4.2452 L22: 3.1082 REMARK 3 L33: 4.7910 L12: 1.1845 REMARK 3 L13: 4.3834 L23: 2.0762 REMARK 3 S TENSOR REMARK 3 S11: 0.2338 S12: -0.1944 S13: 0.0303 REMARK 3 S21: -0.0389 S22: -0.3509 S23: 0.3190 REMARK 3 S31: -0.0671 S32: -0.7459 S33: 0.1443 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.4410 8.5454 30.1954 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.2048 REMARK 3 T33: 0.1525 T12: 0.0008 REMARK 3 T13: -0.0086 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 9.5030 L22: 7.5452 REMARK 3 L33: 4.1174 L12: -5.7224 REMARK 3 L13: -6.0970 L23: 4.5882 REMARK 3 S TENSOR REMARK 3 S11: 0.1665 S12: -0.3724 S13: 0.6222 REMARK 3 S21: -0.1044 S22: 0.0465 S23: -0.2571 REMARK 3 S31: -0.4030 S32: 0.1845 S33: -0.2041 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.6862 -0.5678 12.2197 REMARK 3 T TENSOR REMARK 3 T11: 0.2286 T22: 0.4101 REMARK 3 T33: 0.2109 T12: 0.0762 REMARK 3 T13: 0.0889 T23: 0.0330 REMARK 3 L TENSOR REMARK 3 L11: 0.8992 L22: 4.1757 REMARK 3 L33: 8.8526 L12: -0.9159 REMARK 3 L13: -1.0446 L23: 5.5511 REMARK 3 S TENSOR REMARK 3 S11: 0.2225 S12: 0.6485 S13: 0.0067 REMARK 3 S21: -0.5488 S22: -0.1331 S23: -0.6122 REMARK 3 S31: 0.0525 S32: 0.7239 S33: -0.1788 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6314 -9.1268 13.1725 REMARK 3 T TENSOR REMARK 3 T11: 0.4931 T22: 0.4759 REMARK 3 T33: 0.2770 T12: 0.0913 REMARK 3 T13: 0.0606 T23: -0.1079 REMARK 3 L TENSOR REMARK 3 L11: 6.0427 L22: 3.1100 REMARK 3 L33: 7.4255 L12: 3.8233 REMARK 3 L13: -6.6798 L23: -4.3971 REMARK 3 S TENSOR REMARK 3 S11: -0.5959 S12: 1.7507 S13: -0.8365 REMARK 3 S21: -0.8711 S22: 0.0799 S23: -0.1615 REMARK 3 S31: 1.3516 S32: -0.6073 S33: 0.4333 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN 'B' OR CHAIN 'B') AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8121 1.4142 4.4328 REMARK 3 T TENSOR REMARK 3 T11: 0.2462 T22: 0.2324 REMARK 3 T33: 0.1298 T12: 0.0736 REMARK 3 T13: 0.0515 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 1.9249 L22: 7.3050 REMARK 3 L33: 4.3124 L12: -1.2239 REMARK 3 L13: 2.4868 L23: -1.5229 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: 0.4852 S13: 0.0249 REMARK 3 S21: -0.7996 S22: -0.3828 S23: -0.3322 REMARK 3 S31: 0.0764 S32: 0.3895 S33: 0.2720 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4003 3.6894 3.1328 REMARK 3 T TENSOR REMARK 3 T11: 0.3577 T22: 0.2071 REMARK 3 T33: 0.1370 T12: 0.0938 REMARK 3 T13: -0.0383 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 3.4214 L22: 2.9561 REMARK 3 L33: 6.9369 L12: -0.7816 REMARK 3 L13: 0.1104 L23: 3.2536 REMARK 3 S TENSOR REMARK 3 S11: 0.0655 S12: 0.3480 S13: -0.0802 REMARK 3 S21: -0.8550 S22: -0.3480 S23: 0.1407 REMARK 3 S31: -0.5664 S32: -0.2508 S33: 0.3342 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 6DOH 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_1000234974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-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 : 23-BM-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38071 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 19.814 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.6 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: 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 (%): 50.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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 40.59700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.92150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.59700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.92150 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: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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: 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' -0.043 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 434 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 435 DISTANCE = 6.63 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 ASP A 71 OD2 47.7 REMARK 620 3 ASP A 192 OD1 118.9 78.1 REMARK 620 4 HOH A 333 O 83.9 108.2 90.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 ASP A 71 OD2 44.3 REMARK 620 3 VAL A 72 O 74.8 83.9 REMARK 620 4 ASP A 192 OD1 85.0 59.0 141.0 REMARK 620 5 C b 5 OP1 67.8 105.5 107.7 94.3 REMARK 620 6 G b 6 OP2 148.2 166.9 96.1 117.2 87.0 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 71 OD1 REMARK 620 2 ASP A 132 OD1 149.8 REMARK 620 3 ASP A 132 OD2 111.1 48.6 REMARK 620 4 HOH A 333 O 68.6 98.1 49.8 REMARK 620 5 HOH A 339 O 89.9 67.7 83.0 107.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH b 106 O REMARK 620 2 DT C 4 O4 154.7 REMARK 620 3 DG C 5 O6 88.6 75.0 REMARK 620 4 HOH C 204 O 120.0 53.6 113.5 REMARK 620 5 HOH C 210 O 109.9 88.3 85.5 126.1 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 CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K 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 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 103 DBREF 6DOH A 61 193 UNP Q9KEI9 RNH1_BACHD 61 193 DBREF 6DOH B 1 4 PDB 6DOH 6DOH 1 4 DBREF 6DOH b 5 6 PDB 6DOH 6DOH 5 6 DBREF 6DOH C 1 6 PDB 6DOH 6DOH 1 6 SEQRES 1 A 133 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 133 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 133 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 133 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 133 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 133 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 133 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 133 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 133 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 133 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 133 ALA ASP TYR SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET CA A 201 1 HET K A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET GOL A 208 6 HET GOL A 209 6 HET EDO A 210 4 HET EDO A 211 4 HET GOL A 212 6 HET K C 101 1 HET EDO C 102 4 HET GOL C 103 6 HETNAM CA CALCIUM 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 CA CA 2+ FORMUL 6 K 3(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 4(C3 H8 O3) FORMUL 14 EDO 3(C2 H6 O2) FORMUL 20 HOH *173(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 O3'A U B 4 P A C b 5 1555 1555 1.59 LINK OD1 ASP A 71 CA B CA A 201 1555 1555 2.77 LINK OD2 ASP A 71 CA B CA A 201 1555 1555 2.62 LINK OD1 ASP A 71 K A K A 202 1555 1555 3.01 LINK OD2 ASP A 71 K A K A 202 1555 1555 2.74 LINK OD1 ASP A 71 K B K A 203 1555 1555 2.50 LINK O VAL A 72 K A K A 202 1555 1555 2.55 LINK OD1 ASP A 132 K B K A 203 1555 1555 2.51 LINK OD2 ASP A 132 K B K A 203 1555 1555 2.81 LINK OD1 ASP A 192 CA B CA A 201 1555 1555 2.33 LINK OD1 ASP A 192 K A K A 202 1555 1555 3.47 LINK CA B CA A 201 O HOH A 333 1555 1555 2.38 LINK K A K A 202 OP1A C b 5 1555 1555 2.73 LINK K A K A 202 OP2A G b 6 1555 1555 2.87 LINK K B K A 203 O HOH A 333 1555 1555 3.46 LINK K B K A 203 O HOH A 339 1555 1555 3.02 LINK O HOH b 106 K K C 101 4555 1555 2.99 LINK O4 DT C 4 K K C 101 1555 1555 3.28 LINK O6 DG C 5 K K C 101 1555 1555 2.61 LINK K K C 101 O BHOH C 204 1555 1555 2.52 LINK K K C 101 O HOH C 210 1555 1555 3.02 CISPEP 1 ASN A 77 PRO A 78 0 -2.17 SITE 1 AC1 6 ASP A 71 ASP A 192 K A 202 HOH A 333 SITE 2 AC1 6 HOH A 403 C b 5 SITE 1 AC2 6 ASP A 71 VAL A 72 ASP A 192 CA A 201 SITE 2 AC2 6 C b 5 G b 6 SITE 1 AC3 6 ASP A 71 GLU A 109 ASP A 132 HOH A 339 SITE 2 AC3 6 U B 4 C b 5 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 433 HOH A 435 SITE 1 AC6 2 HIS A 172 HOH A 426 SITE 1 AC7 6 GLU A 66 LEU A 94 LYS A 127 HOH A 307 SITE 2 AC7 6 HOH A 312 HOH A 363 SITE 1 AC8 5 LYS A 143 THR A 173 TYR A 174 EDO A 211 SITE 2 AC8 5 HOH A 311 SITE 1 AC9 3 HOH A 302 HOH A 318 HOH C 203 SITE 1 AD1 6 ARG A 97 LYS A 143 HIS A 172 GOL A 209 SITE 2 AD1 6 HOH A 310 HOH A 344 SITE 1 AD2 9 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AD2 9 GLU A 167 ASN A 170 HOH A 321 HOH A 389 SITE 3 AD2 9 HOH A 409 SITE 1 AD3 5 DT C 4 DG C 5 HOH C 204 HOH C 210 SITE 2 AD3 5 HOH b 106 SITE 1 AD4 4 THR A 148 DT C 4 DG C 5 HOH C 215 SITE 1 AD5 4 ASN A 77 HOH B 102 DG C 2 DA C 3 CRYST1 81.194 37.843 61.829 90.00 96.15 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 0.012316 0.000000 0.001326 0.00000 SCALE2 0.000000 0.026425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016267 0.00000