HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP6 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 80 MM MG2+ AND 75 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 FRAGMENT: CATALYTIC DOMAIN RESIDUES 59-196; 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 CLEAVED 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 CLEAVED 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: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, RNA HYDROLYSIS, IN CRYSTALLO CATALYSIS, KEYWDS 2 METAL DEPENDENT CATALYSIS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 3 11-OCT-23 6DP6 1 LINK REVDAT 2 22-AUG-18 6DP6 1 JRNL REVDAT 1 15-AUG-18 6DP6 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. 1.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 64614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3246 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.0864 - 3.9813 0.98 2916 178 0.1271 0.1503 REMARK 3 2 3.9813 - 3.1641 0.92 2705 137 0.1424 0.1730 REMARK 3 3 3.1641 - 2.7653 0.94 2789 153 0.1656 0.1967 REMARK 3 4 2.7653 - 2.5129 0.95 2786 143 0.1659 0.1646 REMARK 3 5 2.5129 - 2.3331 0.95 2830 133 0.1514 0.1734 REMARK 3 6 2.3331 - 2.1957 0.95 2882 130 0.1654 0.1775 REMARK 3 7 2.1957 - 2.0859 0.91 2684 152 0.1510 0.1748 REMARK 3 8 2.0859 - 1.9952 0.84 2533 138 0.1684 0.1973 REMARK 3 9 1.9952 - 1.9184 0.92 2663 162 0.1754 0.2211 REMARK 3 10 1.9184 - 1.8523 0.90 2677 135 0.1845 0.2249 REMARK 3 11 1.8523 - 1.7944 0.94 2759 165 0.1759 0.2417 REMARK 3 12 1.7944 - 1.7431 0.94 2787 180 0.1751 0.1753 REMARK 3 13 1.7431 - 1.6973 0.95 2808 117 0.1743 0.1614 REMARK 3 14 1.6973 - 1.6559 0.96 2906 121 0.1812 0.1909 REMARK 3 15 1.6559 - 1.6183 0.96 2836 153 0.1892 0.2567 REMARK 3 16 1.6183 - 1.5838 0.96 2893 133 0.1973 0.2248 REMARK 3 17 1.5838 - 1.5522 0.95 2764 175 0.2101 0.2075 REMARK 3 18 1.5522 - 1.5229 0.86 2654 119 0.2363 0.2588 REMARK 3 19 1.5229 - 1.4957 0.80 2343 103 0.2485 0.3131 REMARK 3 20 1.4957 - 1.4703 0.83 2481 160 0.2580 0.2803 REMARK 3 21 1.4703 - 1.4466 0.84 2468 141 0.2715 0.2674 REMARK 3 22 1.4466 - 1.4244 0.81 2454 99 0.2818 0.3431 REMARK 3 23 1.4244 - 1.4034 0.60 1750 119 0.2963 0.3220 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.78 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 : 1.026 2020 REMARK 3 CHIRALITY : 0.071 225 REMARK 3 PLANARITY : 0.007 211 REMARK 3 DIHEDRAL : 24.233 576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4106 -5.6519 17.4687 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.1143 REMARK 3 T33: 0.1033 T12: 0.0162 REMARK 3 T13: 0.0332 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.3085 L22: 2.6653 REMARK 3 L33: 3.7413 L12: -1.8389 REMARK 3 L13: 0.6627 L23: -0.8646 REMARK 3 S TENSOR REMARK 3 S11: 0.1802 S12: 0.1330 S13: -0.2316 REMARK 3 S21: -0.1122 S22: -0.1042 S23: -0.0675 REMARK 3 S31: 0.2323 S32: 0.1887 S33: -0.0796 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.8226 -11.6798 24.1795 REMARK 3 T TENSOR REMARK 3 T11: 0.1873 T22: 0.2098 REMARK 3 T33: 0.2623 T12: 0.0369 REMARK 3 T13: 0.0052 T23: 0.0476 REMARK 3 L TENSOR REMARK 3 L11: 9.3659 L22: 7.9534 REMARK 3 L33: 4.1194 L12: -0.8147 REMARK 3 L13: -6.1348 L23: 1.4294 REMARK 3 S TENSOR REMARK 3 S11: -0.2396 S12: -0.2879 S13: -1.2421 REMARK 3 S21: 0.1853 S22: 0.1090 S23: -0.5104 REMARK 3 S31: 0.4789 S32: 0.2567 S33: 0.2470 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9207 -0.9425 23.7696 REMARK 3 T TENSOR REMARK 3 T11: 0.1261 T22: 0.1094 REMARK 3 T33: 0.1061 T12: 0.0094 REMARK 3 T13: 0.0364 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 5.0271 L22: 0.7987 REMARK 3 L33: 3.5178 L12: -0.0062 REMARK 3 L13: 2.5437 L23: 0.4064 REMARK 3 S TENSOR REMARK 3 S11: 0.0782 S12: -0.2538 S13: -0.0676 REMARK 3 S21: 0.0201 S22: -0.0824 S23: 0.0316 REMARK 3 S31: 0.0912 S32: -0.2028 S33: -0.0018 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0103 9.3863 16.7595 REMARK 3 T TENSOR REMARK 3 T11: 0.2353 T22: 0.1337 REMARK 3 T33: 0.1642 T12: -0.0225 REMARK 3 T13: 0.0418 T23: 0.0373 REMARK 3 L TENSOR REMARK 3 L11: 7.0837 L22: 7.6102 REMARK 3 L33: 6.6469 L12: -6.0873 REMARK 3 L13: -3.4700 L23: 4.0920 REMARK 3 S TENSOR REMARK 3 S11: 0.2577 S12: 0.1367 S13: 0.4942 REMARK 3 S21: -0.3092 S22: -0.0733 S23: -0.6728 REMARK 3 S31: -0.6846 S32: 0.1205 S33: -0.1758 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6603 7.9576 16.0607 REMARK 3 T TENSOR REMARK 3 T11: 0.2195 T22: 0.2083 REMARK 3 T33: 0.1922 T12: 0.1258 REMARK 3 T13: 0.0396 T23: -0.0589 REMARK 3 L TENSOR REMARK 3 L11: 8.0035 L22: 1.2664 REMARK 3 L33: 5.4285 L12: -1.8247 REMARK 3 L13: 2.4325 L23: -2.2132 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.2738 S13: 0.5550 REMARK 3 S21: -0.2081 S22: -0.0655 S23: 0.5161 REMARK 3 S31: -0.1731 S32: -0.3008 S33: 0.0514 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4712 5.8377 25.0144 REMARK 3 T TENSOR REMARK 3 T11: 0.1740 T22: 0.1941 REMARK 3 T33: 0.1551 T12: 0.0298 REMARK 3 T13: 0.0259 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 9.1608 L22: 3.9743 REMARK 3 L33: 5.5074 L12: 4.8281 REMARK 3 L13: 7.0009 L23: 4.1397 REMARK 3 S TENSOR REMARK 3 S11: 0.1451 S12: -0.4412 S13: 0.2328 REMARK 3 S21: 0.1263 S22: -0.2579 S23: 0.1600 REMARK 3 S31: -0.1053 S32: -0.4863 S33: 0.1330 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.7701 -1.0435 17.9308 REMARK 3 T TENSOR REMARK 3 T11: 0.1122 T22: 0.1346 REMARK 3 T33: 0.0847 T12: 0.0555 REMARK 3 T13: -0.0027 T23: 0.0563 REMARK 3 L TENSOR REMARK 3 L11: 3.8213 L22: 3.6953 REMARK 3 L33: 5.8871 L12: -1.0809 REMARK 3 L13: -1.8832 L23: 2.4050 REMARK 3 S TENSOR REMARK 3 S11: 0.1022 S12: 0.2080 S13: -0.0304 REMARK 3 S21: -0.3165 S22: 0.0356 S23: -0.1567 REMARK 3 S31: -0.0297 S32: 0.3023 S33: -0.1580 REMARK 3 TLS GROUP : 8 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): 23.7499 0.7220 5.1563 REMARK 3 T TENSOR REMARK 3 T11: 0.2717 T22: 0.2884 REMARK 3 T33: 0.1314 T12: 0.0748 REMARK 3 T13: 0.0556 T23: 0.0297 REMARK 3 L TENSOR REMARK 3 L11: 1.9089 L22: 6.9353 REMARK 3 L33: 1.1709 L12: 0.1686 REMARK 3 L13: 1.3523 L23: -0.6662 REMARK 3 S TENSOR REMARK 3 S11: 0.0368 S12: 0.3629 S13: 0.0099 REMARK 3 S21: -0.6136 S22: -0.2193 S23: -0.3184 REMARK 3 S31: 0.1095 S32: 0.2063 S33: 0.2041 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4738 3.6164 3.3071 REMARK 3 T TENSOR REMARK 3 T11: 0.3175 T22: 0.2220 REMARK 3 T33: 0.1233 T12: 0.0416 REMARK 3 T13: -0.0133 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 2.4088 L22: 5.1341 REMARK 3 L33: 8.7451 L12: -1.3139 REMARK 3 L13: -2.2784 L23: 5.3133 REMARK 3 S TENSOR REMARK 3 S11: -0.1045 S12: 0.2799 S13: -0.0079 REMARK 3 S21: -0.8720 S22: -0.2898 S23: 0.1579 REMARK 3 S31: -0.3891 S32: -0.1537 S33: 0.3951 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 6DP6 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_1000235012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 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-ID-D 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33053 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.3 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: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 40.91600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.64600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.91600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.64600 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 OE1 GLU A 122 O HOH A 301 1.79 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 -0.127 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 414 DISTANCE = 6.42 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 107.4 REMARK 620 3 HOH A 302 O 169.0 80.6 REMARK 620 4 HOH A 309 O 87.2 87.6 85.6 REMARK 620 5 HOH A 332 O 89.6 87.4 98.4 173.1 REMARK 620 6 C b 5 OP3 155.7 96.8 17.4 92.5 92.9 REMARK 620 7 C b 5 OP1 94.6 156.1 78.9 102.8 83.6 61.8 REMARK 620 8 C b 5 OP1 93.4 157.7 80.0 101.6 84.7 62.9 1.7 REMARK 620 N 1 2 3 4 5 6 7 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 99.5 REMARK 620 3 ASP A 132 OD1 137.2 94.8 REMARK 620 4 ASP A 132 OD2 99.3 151.5 57.1 REMARK 620 5 U B 4 O3' 150.2 86.0 70.5 88.3 REMARK 620 6 C b 5 OP1 91.4 110.0 121.0 90.8 59.5 REMARK 620 7 C b 5 OP1 86.6 112.1 124.5 90.2 64.5 5.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 204 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE1 REMARK 620 2 GLU A 188 OE2 41.1 REMARK 620 3 HOH A 332 O 93.4 52.7 REMARK 620 4 HOH A 362 O 89.0 66.3 62.0 REMARK 620 5 HOH B 107 O 86.5 127.1 179.2 117.2 REMARK 620 6 C b 5 OP2 125.3 114.6 79.8 130.7 100.9 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 ASP A 192 OD2 40.8 REMARK 620 3 HOH A 302 O 52.9 87.3 REMARK 620 4 HOH A 309 O 54.0 91.6 50.7 REMARK 620 5 HOH A 341 O 82.2 54.0 93.5 133.9 REMARK 620 6 G b 6 OP2 99.2 139.8 60.7 49.9 142.7 REMARK 620 N 1 2 3 4 5 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 DG C 5 O6 REMARK 620 2 HOH C 204 O 90.2 REMARK 620 3 HOH C 211 O 84.1 54.5 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 K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K 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 IOD A 207 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 EDO 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 K C 101 DBREF 6DP6 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP6 B 1 4 PDB 6DP6 6DP6 1 4 DBREF 6DP6 b 5 6 PDB 6DP6 6DP6 5 6 DBREF 6DP6 C 1 6 PDB 6DP6 6DP6 1 6 SEQADV 6DP6 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP6 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP6 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP6 MET A 58 UNP Q9KEI9 EXPRESSION TAG 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 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 MG A 201 1 HET MG A 202 1 HET K A 203 1 HET K A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET IOD A 208 1 HET EDO A 209 4 HET EDO A 210 4 HET K C 101 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 3(K 1+) FORMUL 9 IOD 4(I 1-) FORMUL 13 EDO 2(C2 H6 O2) FORMUL 16 HOH *140(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 O3'C U B 4 P C C b 5 1555 1555 1.59 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.99 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.95 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.01 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.08 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.41 LINK OE1 GLU A 188 K B K A 204 1555 1555 3.27 LINK OE2 GLU A 188 K B K A 204 1555 1555 2.87 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.05 LINK OD1 ASP A 192 K C K A 203 1555 1555 2.81 LINK OD2 ASP A 192 K C K A 203 1555 1555 3.30 LINK MG MG A 201 O CHOH A 302 1555 1555 2.02 LINK MG MG A 201 O HOH A 309 1555 1555 2.08 LINK MG MG A 201 O HOH A 332 1555 1555 2.08 LINK MG MG A 201 OP3B C b 5 1555 1555 2.01 LINK MG MG A 201 OP1B C b 5 1555 1555 2.45 LINK MG MG A 201 OP1C C b 5 1555 1555 2.27 LINK MG MG A 202 O3'C U B 4 1555 1555 2.64 LINK MG MG A 202 OP1B C b 5 1555 1555 2.09 LINK MG MG A 202 OP1C C b 5 1555 1555 2.14 LINK K C K A 203 O CHOH A 302 1555 1555 3.09 LINK K C K A 203 O HOH A 309 1555 1555 3.39 LINK K C K A 203 O HOH A 341 1555 1555 2.60 LINK K C K A 203 OP2 G b 6 1555 1555 2.85 LINK K B K A 204 O HOH A 332 1555 1555 3.18 LINK K B K A 204 O HOH A 362 1555 1555 3.18 LINK K B K A 204 O HOH B 107 1555 1555 2.72 LINK K B K A 204 OP2B C b 5 1555 1555 2.56 LINK O6 DG C 5 K A K C 101 1555 1555 2.58 LINK K A K C 101 O HOH C 204 1555 1555 2.95 LINK K A K C 101 O HOH C 211 1555 1555 3.29 CISPEP 1 ASN A 77 PRO A 78 0 -2.07 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 302 HOH A 309 SITE 2 AC1 6 HOH A 332 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 9 ASP A 192 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 9 HOH A 302 HOH A 341 C b 5 G b 6 SITE 3 AC3 9 HOH b 101 SITE 1 AC4 3 GLU A 188 HOH B 107 C b 5 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 2 HOH A 393 HOH A 414 SITE 1 AC7 1 HIS A 172 SITE 1 AC8 3 GLU A 66 SER A 125 LYS A 127 SITE 1 AC9 6 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AC9 6 GLU A 167 HOH A 378 SITE 1 AD1 3 DG C 5 HOH C 203 HOH C 204 CRYST1 81.832 37.292 62.607 90.00 96.71 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 0.012220 0.000000 0.001438 0.00000 SCALE2 0.000000 0.026815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016083 0.00000