HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP3 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 10 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 6DP3 1 LINK REVDAT 2 22-AUG-18 6DP3 1 JRNL REVDAT 1 15-AUG-18 6DP3 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. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 32658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1646 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 19.0933 - 3.3399 0.97 2631 126 0.1610 0.1825 REMARK 3 2 3.3399 - 2.6532 1.00 2618 143 0.1558 0.1773 REMARK 3 3 2.6532 - 2.3185 1.00 2615 145 0.1606 0.2042 REMARK 3 4 2.3185 - 2.1068 1.00 2601 136 0.1559 0.1838 REMARK 3 5 2.1068 - 1.9560 1.00 2570 144 0.1557 0.1875 REMARK 3 6 1.9560 - 1.8407 1.00 2614 155 0.1735 0.2067 REMARK 3 7 1.8407 - 1.7486 1.00 2596 131 0.1876 0.2348 REMARK 3 8 1.7486 - 1.6726 1.00 2563 131 0.1991 0.2089 REMARK 3 9 1.6726 - 1.6082 1.00 2574 148 0.2140 0.2561 REMARK 3 10 1.6082 - 1.5527 0.99 2582 124 0.2352 0.2937 REMARK 3 11 1.5527 - 1.5042 0.99 2558 137 0.2661 0.2501 REMARK 3 12 1.5042 - 1.4612 0.97 2490 126 0.2898 0.3243 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) : 21.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.30 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 1528 REMARK 3 ANGLE : 1.085 2078 REMARK 3 CHIRALITY : 0.074 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 22.993 598 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): 25.2912 -5.5831 17.3406 REMARK 3 T TENSOR REMARK 3 T11: 0.1584 T22: 0.1060 REMARK 3 T33: 0.1197 T12: 0.0176 REMARK 3 T13: 0.0225 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 8.0419 L22: 1.8853 REMARK 3 L33: 3.5163 L12: -1.9462 REMARK 3 L13: 1.6142 L23: -1.1005 REMARK 3 S TENSOR REMARK 3 S11: 0.1641 S12: -0.0419 S13: -0.2787 REMARK 3 S21: -0.1208 S22: -0.0719 S23: -0.0358 REMARK 3 S31: 0.2249 S32: 0.2256 S33: -0.1174 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9060 -11.5459 23.9589 REMARK 3 T TENSOR REMARK 3 T11: 0.2253 T22: 0.1797 REMARK 3 T33: 0.2860 T12: 0.0657 REMARK 3 T13: 0.0444 T23: 0.0699 REMARK 3 L TENSOR REMARK 3 L11: 5.3516 L22: 2.4540 REMARK 3 L33: 7.3956 L12: -2.9591 REMARK 3 L13: -5.9838 L23: 2.7949 REMARK 3 S TENSOR REMARK 3 S11: -0.1889 S12: -0.3499 S13: -0.9460 REMARK 3 S21: -0.1025 S22: 0.0273 S23: -0.2331 REMARK 3 S31: 0.8057 S32: 0.3862 S33: 0.2040 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7651 -1.1781 23.1848 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.0956 REMARK 3 T33: 0.1077 T12: 0.0095 REMARK 3 T13: 0.0193 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 4.7622 L22: 0.8393 REMARK 3 L33: 4.2495 L12: -0.1818 REMARK 3 L13: 2.7640 L23: -0.1784 REMARK 3 S TENSOR REMARK 3 S11: 0.1216 S12: -0.2461 S13: -0.1372 REMARK 3 S21: -0.0080 S22: -0.0706 S23: 0.0311 REMARK 3 S31: 0.1592 S32: -0.1514 S33: -0.0363 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.1290 9.2272 16.5008 REMARK 3 T TENSOR REMARK 3 T11: 0.2565 T22: 0.1524 REMARK 3 T33: 0.1734 T12: -0.0072 REMARK 3 T13: 0.0155 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 8.8856 L22: 5.4896 REMARK 3 L33: 4.8794 L12: -3.1471 REMARK 3 L13: -0.4850 L23: 4.7132 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: 0.0977 S13: 0.3602 REMARK 3 S21: -0.2843 S22: -0.0132 S23: -0.2852 REMARK 3 S31: -0.7135 S32: 0.1545 S33: -0.0366 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7487 7.8561 15.8590 REMARK 3 T TENSOR REMARK 3 T11: 0.1977 T22: 0.1586 REMARK 3 T33: 0.1905 T12: 0.1197 REMARK 3 T13: 0.0306 T23: -0.0558 REMARK 3 L TENSOR REMARK 3 L11: 7.2184 L22: 2.8266 REMARK 3 L33: 7.0139 L12: -0.2792 REMARK 3 L13: 3.8594 L23: -0.5966 REMARK 3 S TENSOR REMARK 3 S11: -0.1067 S12: 0.0553 S13: 0.4938 REMARK 3 S21: -0.1912 S22: -0.0261 S23: 0.5636 REMARK 3 S31: -0.2582 S32: -0.4986 S33: 0.0957 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6973 5.9057 24.7096 REMARK 3 T TENSOR REMARK 3 T11: 0.1745 T22: 0.2092 REMARK 3 T33: 0.1684 T12: 0.0467 REMARK 3 T13: 0.0278 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 5.0111 L22: 2.8218 REMARK 3 L33: 8.1766 L12: 3.4609 REMARK 3 L13: 6.3000 L23: 4.2171 REMARK 3 S TENSOR REMARK 3 S11: 0.0709 S12: -0.5576 S13: 0.1603 REMARK 3 S21: 0.1022 S22: -0.2481 S23: 0.1005 REMARK 3 S31: -0.0605 S32: -0.5072 S33: 0.1624 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1087 -1.3851 17.2578 REMARK 3 T TENSOR REMARK 3 T11: 0.1560 T22: 0.1544 REMARK 3 T33: 0.0951 T12: 0.0692 REMARK 3 T13: 0.0054 T23: 0.0580 REMARK 3 L TENSOR REMARK 3 L11: 4.4790 L22: 3.5829 REMARK 3 L33: 5.3420 L12: -1.3893 REMARK 3 L13: -2.0348 L23: 2.2953 REMARK 3 S TENSOR REMARK 3 S11: 0.1673 S12: 0.1756 S13: -0.1402 REMARK 3 S21: -0.4218 S22: -0.0519 S23: -0.2466 REMARK 3 S31: -0.0580 S32: 0.2907 S33: -0.1537 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): 23.9838 0.8360 4.9373 REMARK 3 T TENSOR REMARK 3 T11: 0.3368 T22: 0.2946 REMARK 3 T33: 0.1889 T12: 0.0879 REMARK 3 T13: 0.0783 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 2.2577 L22: 1.8464 REMARK 3 L33: 2.3652 L12: -0.5501 REMARK 3 L13: 2.0127 L23: -1.1763 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: 0.2538 S13: -0.1748 REMARK 3 S21: -0.6727 S22: -0.2842 S23: -0.3572 REMARK 3 S31: 0.3100 S32: 0.3146 S33: 0.3076 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6219 3.4238 3.0843 REMARK 3 T TENSOR REMARK 3 T11: 0.2628 T22: 0.1931 REMARK 3 T33: 0.1359 T12: 0.0600 REMARK 3 T13: -0.0193 T23: 0.0280 REMARK 3 L TENSOR REMARK 3 L11: 3.1737 L22: 7.9469 REMARK 3 L33: 6.3234 L12: -0.1236 REMARK 3 L13: -1.9363 L23: 4.7417 REMARK 3 S TENSOR REMARK 3 S11: -0.0839 S12: 0.3008 S13: 0.0085 REMARK 3 S21: -0.8561 S22: -0.2623 S23: 0.2023 REMARK 3 S31: -0.4096 S32: -0.1568 S33: 0.3466 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 6DP3 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_1000235011. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-17 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-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 : 32665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 19.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 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 (%): 49.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 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 40.76500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.05400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.76500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.05400 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: 7090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 O3' C B 2 O HOH B 101 2.01 REMARK 500 OH TYR A 83 O HOH A 301 2.14 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 -0.163 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C B 2 C6 - N1 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 C B 2 C2 - N1 - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 108.5 REMARK 620 3 HOH A 302 O 166.4 76.7 REMARK 620 4 HOH A 307 O 88.4 91.9 104.2 REMARK 620 5 HOH A 317 O 88.0 83.4 80.0 172.9 REMARK 620 6 C b 5 OP3 156.0 95.5 21.7 92.9 92.8 REMARK 620 7 C b 5 OP1 94.2 156.9 82.1 84.3 102.0 62.1 REMARK 620 8 C b 5 OP1 92.0 159.4 83.7 87.0 99.2 64.1 3.5 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 97.9 REMARK 620 3 ASP A 132 OD1 136.8 95.6 REMARK 620 4 ASP A 132 OD2 101.4 152.8 57.3 REMARK 620 5 U B 4 O3' 146.2 85.4 75.6 89.0 REMARK 620 6 C b 5 OP1 90.5 107.0 124.1 91.8 56.9 REMARK 620 7 C b 5 OP1 84.4 108.3 129.1 92.5 62.9 6.1 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 41.3 REMARK 620 3 HOH A 307 O 84.6 45.3 REMARK 620 4 C b 5 OP2 127.1 115.3 78.8 REMARK 620 N 1 2 3 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 40.6 REMARK 620 3 HOH A 302 O 50.7 84.4 REMARK 620 4 HOH A 317 O 53.1 91.4 48.9 REMARK 620 5 HOH A 325 O 80.5 53.3 89.3 130.0 REMARK 620 6 G b 6 OP2 100.2 140.8 60.7 52.8 135.5 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 203 O 89.7 REMARK 620 3 HOH C 207 O 94.3 158.1 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 GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues EDO A 213 and GOL A REMARK 800 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues EDO C 102 and GOL C REMARK 800 103 DBREF 6DP3 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP3 B 1 4 PDB 6DP3 6DP3 1 4 DBREF 6DP3 b 5 6 PDB 6DP3 6DP3 5 6 DBREF 6DP3 C 1 6 PDB 6DP3 6DP3 1 6 SEQADV 6DP3 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP3 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP3 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP3 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 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 EDO A 214 4 HET EDO A 215 4 HET EDO A 216 4 HET GOL A 217 6 HET GOL A 218 6 HET GOL A 219 6 HET GOL A 220 6 HET K C 101 1 HET EDO C 102 4 HET GOL C 103 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 3(K 1+) FORMUL 9 IOD 3(I 1-) FORMUL 12 GOL 9(C3 H8 O3) FORMUL 16 EDO 6(C2 H6 O2) FORMUL 28 HOH *110(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 C1 EDO A 213 O3 GOL A 218 1555 1555 1.38 LINK O3'C U B 4 P C C b 5 1555 1555 1.59 LINK O2 AEDO C 102 C1 GOL C 103 1555 1555 1.38 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.99 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.93 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.09 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.03 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 2.83 LINK OE2 GLU A 188 K B K A 204 1555 1555 3.27 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.06 LINK OD1 ASP A 192 K C K A 203 1555 1555 2.80 LINK OD2 ASP A 192 K C K A 203 1555 1555 3.34 LINK MG MG A 201 O CHOH A 302 1555 1555 2.02 LINK MG MG A 201 O HOH A 307 1555 1555 2.06 LINK MG MG A 201 O HOH A 317 1555 1555 2.06 LINK MG MG A 201 OP3B C b 5 1555 1555 2.02 LINK MG MG A 201 OP1B C b 5 1555 1555 2.44 LINK MG MG A 201 OP1C C b 5 1555 1555 2.26 LINK MG MG A 202 O3'C U B 4 1555 1555 2.62 LINK MG MG A 202 OP1B C b 5 1555 1555 2.11 LINK MG MG A 202 OP1C C b 5 1555 1555 2.15 LINK K C K A 203 O CHOH A 302 1555 1555 3.08 LINK K C K A 203 O HOH A 317 1555 1555 3.26 LINK K C K A 203 O HOH A 325 1555 1555 2.61 LINK K C K A 203 OP2 G b 6 1555 1555 2.86 LINK K B K A 204 O HOH A 307 1555 1555 3.24 LINK K B K A 204 OP2B C b 5 1555 1555 2.54 LINK O6 DG C 5 K B K C 101 1555 1555 2.55 LINK K B K C 101 O BHOH C 203 1555 1555 3.42 LINK K B K C 101 O BHOH C 207 1555 1555 3.02 CISPEP 1 ASN A 77 PRO A 78 0 -0.41 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 302 HOH A 307 SITE 2 AC1 6 HOH A 317 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 8 ASP A 192 TYR A 193 GLY A 194 ARG A 195 SITE 2 AC3 8 LYS A 196 HOH A 302 HOH A 325 G b 6 SITE 1 AC4 2 GLU A 188 C b 5 SITE 1 AC5 6 GLY A 76 ASN A 77 PRO A 78 HOH A 305 SITE 2 AC5 6 DG C 2 DA C 3 SITE 1 AC6 8 TYR A 83 LEU A 111 VAL A 114 HIS A 115 SITE 2 AC6 8 ARG A 118 ALA A 165 HOH A 301 HOH A 319 SITE 1 AC7 8 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AC7 8 GLU A 167 ASN A 170 HOH A 334 HOH A 358 SITE 1 AC8 7 ARG A 97 LEU A 169 ASN A 170 HIS A 172 SITE 2 AC8 7 THR A 173 GOL A 219 HOH A 328 SITE 1 AC9 3 GLU A 66 SER A 125 LYS A 127 SITE 1 AD1 3 LYS A 121 GLU A 122 ASN A 124 SITE 1 AD2 5 TRP A 65 LYS A 89 ARG A 151 ASN A 152 SITE 2 AD2 5 ALA A 156 SITE 1 AD3 2 ASN A 152 GLU A 154 SITE 1 AD4 5 GLU A 122 ARG A 123 ASP A 163 GLU A 166 SITE 2 AD4 5 HOH A 304 SITE 1 AD5 6 LYS A 143 HIS A 172 THR A 173 TYR A 174 SITE 2 AD5 6 GOL A 211 HOH A 364 SITE 1 AD6 4 LYS A 141 ILE A 178 LEU A 179 LYS A 180 SITE 1 AD7 3 DG C 5 EDO C 102 HOH C 207 SITE 1 AD8 8 GLU A 62 ILE A 63 TRP A 65 SER A 147 SITE 2 AD8 8 LEU A 149 VAL A 150 ARG A 151 HOH A 303 SITE 1 AD9 6 THR A 148 LYS A 196 DT C 4 DG C 5 SITE 2 AD9 6 K C 101 HOH C 207 CRYST1 81.530 38.108 61.723 90.00 96.04 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 0.012265 0.000000 0.001298 0.00000 SCALE2 0.000000 0.026241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016292 0.00000