HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DPE TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 20 MM MN2+ AND 200 MM K+ FOR 40 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 13 CHAIN: b; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 17 CHAIN: C; COMPND 18 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: 469008; 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: SYNTHETIC; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 23 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 6DPE 1 LINK REVDAT 1 15-AUG-18 6DPE 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. 1.56 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 24877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1211 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 19.2405 - 3.2324 0.95 2792 143 0.1312 0.1773 REMARK 3 2 3.2324 - 2.5676 0.92 2643 121 0.1671 0.2019 REMARK 3 3 2.5676 - 2.2436 0.94 2614 151 0.1855 0.2143 REMARK 3 4 2.2436 - 2.0387 0.95 2718 118 0.1920 0.2567 REMARK 3 5 2.0387 - 1.8927 0.96 2722 131 0.2137 0.2646 REMARK 3 6 1.8927 - 1.7812 0.96 2705 144 0.2069 0.2505 REMARK 3 7 1.7812 - 1.6921 0.97 2744 140 0.2177 0.2584 REMARK 3 8 1.6921 - 1.6185 0.97 2703 148 0.2462 0.2883 REMARK 3 9 1.6185 - 1.5562 0.73 2025 115 0.2558 0.3037 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.69 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 1466 REMARK 3 ANGLE : 0.980 2020 REMARK 3 CHIRALITY : 0.055 219 REMARK 3 PLANARITY : 0.007 211 REMARK 3 DIHEDRAL : 19.186 831 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.690 -4.005 18.215 REMARK 3 T TENSOR REMARK 3 T11: 0.2452 T22: 0.5572 REMARK 3 T33: 0.3202 T12: 0.0849 REMARK 3 T13: 0.0446 T23: 0.0698 REMARK 3 L TENSOR REMARK 3 L11: 5.9657 L22: 6.1318 REMARK 3 L33: 4.0436 L12: -0.6129 REMARK 3 L13: -0.9750 L23: -4.1665 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.6731 S13: 0.1779 REMARK 3 S21: -0.6018 S22: -0.7802 S23: -1.1761 REMARK 3 S31: 0.1307 S32: 2.0157 S33: 0.7419 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.380 -6.365 15.916 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.1839 REMARK 3 T33: 0.1651 T12: 0.0045 REMARK 3 T13: -0.0105 T23: -0.0132 REMARK 3 L TENSOR REMARK 3 L11: 5.0159 L22: 0.2590 REMARK 3 L33: 4.4741 L12: -0.7129 REMARK 3 L13: 4.7372 L23: -0.6836 REMARK 3 S TENSOR REMARK 3 S11: 0.3524 S12: 0.1683 S13: -0.4483 REMARK 3 S21: -0.0309 S22: -0.1241 S23: 0.1125 REMARK 3 S31: 0.3558 S32: -0.0501 S33: -0.3001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.152 -11.609 23.333 REMARK 3 T TENSOR REMARK 3 T11: 0.2784 T22: 0.1966 REMARK 3 T33: 0.2963 T12: 0.0665 REMARK 3 T13: -0.0234 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 7.3558 L22: 6.1738 REMARK 3 L33: 9.1665 L12: -1.1070 REMARK 3 L13: -7.6739 L23: 1.2523 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: -0.3530 S13: -1.4911 REMARK 3 S21: 0.1083 S22: -0.1932 S23: -0.2370 REMARK 3 S31: 0.7065 S32: 0.5894 S33: 0.2223 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.412 -5.119 18.115 REMARK 3 T TENSOR REMARK 3 T11: 0.2342 T22: 0.3418 REMARK 3 T33: 0.2220 T12: 0.0094 REMARK 3 T13: -0.0215 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 5.0125 L22: 2.3900 REMARK 3 L33: 2.6703 L12: -1.4528 REMARK 3 L13: 1.3034 L23: 1.2896 REMARK 3 S TENSOR REMARK 3 S11: 0.0200 S12: -0.0874 S13: -0.1673 REMARK 3 S21: -0.1001 S22: 0.3097 S23: 0.4804 REMARK 3 S31: 0.1308 S32: -1.0839 S33: -0.3820 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.121 0.615 23.394 REMARK 3 T TENSOR REMARK 3 T11: 0.1215 T22: 0.1238 REMARK 3 T33: 0.1143 T12: -0.0126 REMARK 3 T13: 0.0313 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 6.3058 L22: 3.4759 REMARK 3 L33: 5.4400 L12: -1.5002 REMARK 3 L13: 4.1022 L23: 0.7025 REMARK 3 S TENSOR REMARK 3 S11: -0.0035 S12: -0.2716 S13: -0.0836 REMARK 3 S21: 0.1193 S22: -0.0405 S23: -0.0009 REMARK 3 S31: -0.0631 S32: -0.2580 S33: 0.0420 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 123:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.668 3.768 20.866 REMARK 3 T TENSOR REMARK 3 T11: 0.1886 T22: 0.1118 REMARK 3 T33: 0.1398 T12: -0.0485 REMARK 3 T13: 0.0349 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 4.9484 L22: 1.9516 REMARK 3 L33: 5.8233 L12: -2.4499 REMARK 3 L13: 2.3855 L23: 0.3699 REMARK 3 S TENSOR REMARK 3 S11: 0.1886 S12: 0.0622 S13: 0.2108 REMARK 3 S21: -0.1959 S22: -0.1822 S23: -0.1561 REMARK 3 S31: -0.2937 S32: 0.0969 S33: 0.0236 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.027 9.496 15.543 REMARK 3 T TENSOR REMARK 3 T11: 0.4109 T22: 0.4292 REMARK 3 T33: 0.2618 T12: 0.3261 REMARK 3 T13: -0.0314 T23: -0.1081 REMARK 3 L TENSOR REMARK 3 L11: 6.8701 L22: 2.6653 REMARK 3 L33: 2.8693 L12: 3.2462 REMARK 3 L13: 2.0155 L23: -0.3821 REMARK 3 S TENSOR REMARK 3 S11: 0.3118 S12: 0.3255 S13: 0.5127 REMARK 3 S21: -0.1943 S22: -0.4891 S23: 0.4817 REMARK 3 S31: -0.5515 S32: -0.5205 S33: -0.0894 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 153:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.291 5.023 22.806 REMARK 3 T TENSOR REMARK 3 T11: 0.2052 T22: 0.3635 REMARK 3 T33: 0.1844 T12: 0.0890 REMARK 3 T13: 0.0250 T23: -0.0874 REMARK 3 L TENSOR REMARK 3 L11: 4.1710 L22: 6.0399 REMARK 3 L33: 5.7770 L12: 0.2539 REMARK 3 L13: 3.2062 L23: -0.7451 REMARK 3 S TENSOR REMARK 3 S11: 0.2119 S12: -0.2985 S13: 0.1205 REMARK 3 S21: -0.1876 S22: -0.4744 S23: 0.5900 REMARK 3 S31: -0.0417 S32: -0.9429 S33: 0.2314 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.437 8.552 29.541 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.1989 REMARK 3 T33: 0.2019 T12: 0.0073 REMARK 3 T13: 0.0203 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 6.0435 L22: 4.2984 REMARK 3 L33: 5.0791 L12: -4.2425 REMARK 3 L13: -1.6309 L23: 3.6226 REMARK 3 S TENSOR REMARK 3 S11: 0.0686 S12: -0.5878 S13: 0.4744 REMARK 3 S21: 0.1383 S22: 0.2202 S23: -0.2312 REMARK 3 S31: -0.2863 S32: 0.3228 S33: -0.3246 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.314 -0.793 11.655 REMARK 3 T TENSOR REMARK 3 T11: 0.2491 T22: 0.3339 REMARK 3 T33: 0.1648 T12: 0.0630 REMARK 3 T13: 0.0556 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.0803 L22: 7.9365 REMARK 3 L33: 6.0323 L12: 0.8014 REMARK 3 L13: 1.9537 L23: 5.1650 REMARK 3 S TENSOR REMARK 3 S11: 0.1924 S12: 0.5638 S13: -0.0642 REMARK 3 S21: -0.6758 S22: -0.1072 S23: -0.5476 REMARK 3 S31: -0.3479 S32: 0.3212 S33: -0.1328 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.128 -9.715 10.960 REMARK 3 T TENSOR REMARK 3 T11: 0.2645 T22: 0.1955 REMARK 3 T33: 0.1688 T12: 0.0938 REMARK 3 T13: -0.0024 T23: -0.0284 REMARK 3 L TENSOR REMARK 3 L11: 4.3495 L22: 7.9189 REMARK 3 L33: 6.5302 L12: 4.8733 REMARK 3 L13: -0.8542 L23: 2.9282 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: 0.1248 S13: -0.1263 REMARK 3 S21: -0.0615 S22: 0.0652 S23: -0.0960 REMARK 3 S31: 0.2705 S32: 0.0891 S33: -0.0138 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) OR ( CHAIN B AND RESID 5:6 REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.709 1.178 4.186 REMARK 3 T TENSOR REMARK 3 T11: 0.3097 T22: 0.3389 REMARK 3 T33: 0.1578 T12: 0.0982 REMARK 3 T13: 0.0564 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 1.9100 L22: 6.0824 REMARK 3 L33: 3.7248 L12: -2.2123 REMARK 3 L13: 2.3013 L23: -0.8397 REMARK 3 S TENSOR REMARK 3 S11: 0.1170 S12: 0.4762 S13: 0.1773 REMARK 3 S21: -0.6885 S22: -0.3983 S23: -0.4089 REMARK 3 S31: -0.0191 S32: 0.0754 S33: 0.2822 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.235 3.488 2.762 REMARK 3 T TENSOR REMARK 3 T11: 0.4683 T22: 0.3095 REMARK 3 T33: 0.1559 T12: 0.1195 REMARK 3 T13: -0.0260 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 2.5152 L22: 5.0897 REMARK 3 L33: 3.8230 L12: -0.8002 REMARK 3 L13: -2.5720 L23: 2.7122 REMARK 3 S TENSOR REMARK 3 S11: -0.0787 S12: 0.3186 S13: -0.0918 REMARK 3 S21: -0.8623 S22: -0.2205 S23: 0.1947 REMARK 3 S31: -0.7810 S32: -0.2423 S33: 0.3079 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 6DPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 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 : 24895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 19.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.9 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: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 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 40.49050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.23900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.49050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.23900 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: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 400 REMARK 400 COMPOUND REMARK 400 NOTE THAT CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) AT THE POSITION REMARK 400 4-5, WHERE THE CLEAVAGE OCCURS 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 MN MN A 203 O HOH A 309 1.68 REMARK 500 OH TYR A 174 O HOH A 301 2.05 REMARK 500 O HOH A 410 O HOH A 413 2.13 REMARK 500 O 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 407 O HOH C 113 4555 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C b 5 P C b 5 OP3 -0.101 REMARK 500 DG C 2 O3' DG C 2 C3' -0.041 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 441 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 442 DISTANCE = 6.83 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 109.0 REMARK 620 3 HOH A 334 O 88.6 83.9 REMARK 620 4 HOH A 343 O 86.5 85.4 166.0 REMARK 620 5 C b 5 OP3 156.1 94.6 90.3 99.4 REMARK 620 6 C b 5 OP1 96.1 152.4 85.6 107.9 60.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 98.3 REMARK 620 3 ASP A 132 OD1 135.5 92.1 REMARK 620 4 ASP A 132 OD2 102.5 148.4 56.5 REMARK 620 5 C b 5 OP1 98.7 110.7 117.7 89.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 163 OD1 REMARK 620 2 GLU A 166 OE1 99.4 REMARK 620 3 HOH A 330 O 108.8 151.8 REMARK 620 4 HOH A 402 O 82.3 123.8 63.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 205 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 HOH A 334 O 49.9 REMARK 620 3 HOH A 371 O 64.6 58.1 REMARK 620 4 HOH B 209 O 117.8 166.9 124.2 REMARK 620 5 C b 5 OP2 109.0 81.3 132.3 101.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 196 O REMARK 620 2 HOH A 370 O 87.0 REMARK 620 3 HOH C 102 O 89.6 82.7 REMARK 620 4 HOH C 110 O 175.3 97.7 91.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 211 O REMARK 620 2 HOH C 101 O 159.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD B 102 DBREF 6DPE A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DPE B 1 4 PDB 6DPE 6DPE 1 4 DBREF 6DPE b 5 6 PDB 6DPE 6DPE 5 6 DBREF 6DPE C 1 6 PDB 6DPE 6DPE 1 6 SEQRES 1 A 136 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 136 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 136 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 136 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 136 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 136 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 136 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 136 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 136 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 136 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 136 ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MN A 201 1 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET K A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET IOD A 208 1 HET IOD A 209 1 HET GOL A 210 6 HET GOL A 211 6 HET GOL A 212 6 HET EDO A 213 4 HET EDO A 214 4 HET EDO A 215 4 HET EDO A 216 4 HET PGE A 217 10 HET MN B 101 1 HET IOD B 102 1 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 5(MN 2+) FORMUL 9 K K 1+ FORMUL 10 IOD 5(I 1-) FORMUL 14 GOL 3(C3 H8 O3) FORMUL 17 EDO 4(C2 H6 O2) FORMUL 21 PGE C6 H14 O4 FORMUL 24 HOH *167(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 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 OD2 ASP A 71 MN MN A 201 1555 1555 2.10 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.12 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.05 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.04 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.50 LINK OD1 ASP A 163 MN MN A 203 1555 1555 2.39 LINK OE1 GLU A 166 MN MN A 203 1555 1555 2.04 LINK OE2 GLU A 188 K K A 205 1555 1555 3.00 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.14 LINK O LYS A 196 MN MN A 204 1555 1555 2.17 LINK MN MN A 201 O HOH A 334 1555 1555 2.11 LINK MN MN A 201 O HOH A 343 1555 1555 2.07 LINK MN MN A 201 OP3 C b 5 1555 1555 2.17 LINK MN MN A 201 OP1 C b 5 1555 1555 2.60 LINK MN MN A 202 OP1 C b 5 1555 1555 2.04 LINK MN MN A 203 O HOH A 330 1555 4556 2.36 LINK MN MN A 203 O HOH A 402 1555 1555 2.40 LINK MN MN A 204 O HOH A 370 1555 1555 2.25 LINK MN MN A 204 O HOH C 102 1555 4545 2.25 LINK MN MN A 204 O HOH C 110 1555 4545 2.05 LINK K K A 205 O HOH A 334 1555 1555 3.37 LINK K K A 205 O HOH A 371 1555 1555 3.23 LINK K K A 205 O HOH B 209 1555 1555 2.62 LINK K K A 205 OP2 C b 5 1555 1555 2.70 LINK MN MN B 101 O HOH B 211 1555 1555 2.70 LINK MN MN B 101 O HOH C 101 1555 4545 2.30 CISPEP 1 ASN A 77 PRO A 78 0 4.60 SITE 1 AC1 5 ASP A 71 ASP A 192 HOH A 334 HOH A 343 SITE 2 AC1 5 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 6 ASP A 163 GLU A 166 HOH A 309 HOH A 327 SITE 2 AC3 6 HOH A 330 HOH A 402 SITE 1 AC4 4 LYS A 196 HOH A 370 HOH C 102 HOH C 110 SITE 1 AC5 4 GLU A 188 U B 4 HOH B 209 C b 5 SITE 1 AC6 1 TYR A 83 SITE 1 AC7 2 ILE A 64 HOH A 442 SITE 1 AC8 6 GLY A 76 ASN A 77 PRO A 78 HOH A 307 SITE 2 AC8 6 DG C 2 DA C 3 SITE 1 AC9 7 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AC9 7 ASN A 170 GOL A 212 HOH A 326 SITE 1 AD1 5 HIS A 115 ARG A 118 ASN A 170 GOL A 211 SITE 2 AD1 5 HOH A 312 SITE 1 AD2 4 LYS A 143 THR A 173 TYR A 174 HOH A 318 SITE 1 AD3 3 THR A 148 DT C 4 DG C 5 SITE 1 AD4 3 GLU A 66 LEU A 94 LYS A 127 SITE 1 AD5 4 GLU A 62 ILE A 63 TRP A 65 HOH A 345 SITE 1 AD6 8 PRO A 78 THR A 148 LEU A 149 VAL A 150 SITE 2 AD6 8 ASN A 152 GLU A 154 HOH C 104 HOH C 108 SITE 1 AD7 4 LYS A 196 HOH B 211 HOH C 101 G b 6 SITE 1 AD8 1 HOH A 380 CRYST1 80.981 38.478 60.610 90.00 96.05 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 0.012349 0.000000 0.001308 0.00000 SCALE2 0.000000 0.025989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016591 0.00000